Starting phenix.real_space_refine on Tue Jun 10 16:27:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.map" model { file = "/net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8riz_19192/06_2025/8riz_19192.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 7431 2.51 5 N 2021 2.21 5 O 2323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11862 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "K" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2448 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2453 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 8, 'TRANS': 302} Chain breaks: 1 Chain: "T" Number of atoms: 74 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 37 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Conformer: "B" Number of residues, atoms: 5, 37 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AILE T 920 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE T 920 " occ=0.50 residue: pdb=" N AALA T 921 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA T 921 " occ=0.50 residue: pdb=" N ALYS T 922 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS T 922 " occ=0.50 residue: pdb=" N APRO T 923 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO T 923 " occ=0.50 residue: pdb=" N AILE T 924 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE T 924 " occ=0.50 Time building chain proxies: 7.75, per 1000 atoms: 0.65 Number of scatterers: 11862 At special positions: 0 Unit cell: (86.64, 128.877, 146.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 9 15.00 Mg 2 11.99 O 2323 8.00 N 2021 7.00 C 7431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 16 sheets defined 44.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.301A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 80 removed outlier: 4.484A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.583A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.598A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.942A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.572A pdb=" N ARG B 243 " --> pdb=" O THR B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.904A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.783A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.923A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.843A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.687A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.562A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.689A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.805A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.864A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.950A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.516A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.017A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.315A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.278A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 removed outlier: 4.035A pdb=" N ASN K 24 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 66 removed outlier: 3.671A pdb=" N VAL K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 74 removed outlier: 3.663A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 119 through 122 removed outlier: 3.650A pdb=" N MET K 122 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 119 through 122' Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 237 through 241 removed outlier: 3.553A pdb=" N LYS K 240 " --> pdb=" O LYS K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 271 Processing helix chain 'K' and resid 280 through 286 Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 308 through 323 removed outlier: 4.102A pdb=" N ALA K 322 " --> pdb=" O PHE K 318 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS K 323 " --> pdb=" O GLY K 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.612A pdb=" N VAL L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 76 removed outlier: 4.890A pdb=" N LYS L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 96 Processing helix chain 'L' and resid 106 through 123 Processing helix chain 'L' and resid 175 through 191 removed outlier: 3.537A pdb=" N VAL L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 203 Processing helix chain 'L' and resid 256 through 271 Processing helix chain 'L' and resid 280 through 290 removed outlier: 3.619A pdb=" N ARG L 284 " --> pdb=" O SER L 280 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP L 288 " --> pdb=" O ARG L 284 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER L 289 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 323 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.416A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 272 through 273 removed outlier: 6.758A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.153A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.549A pdb=" N ASN A 380 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.830A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN K 78 " --> pdb=" O ARG K 295 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR K 297 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU K 127 " --> pdb=" O GLU K 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.830A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN K 78 " --> pdb=" O ARG K 295 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR K 297 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU K 127 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG K 171 " --> pdb=" O VAL K 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.660A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL K 39 " --> pdb=" O TYR K 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 155 through 157 Processing sheet with id=AB3, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AB4, first strand: chain 'L' and resid 50 through 52 removed outlier: 7.472A pdb=" N VAL L 11 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE L 52 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS L 13 " --> pdb=" O PHE L 52 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS L 10 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE L 300 " --> pdb=" O LYS L 10 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N MET L 12 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS L 302 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG L 14 " --> pdb=" O CYS L 302 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR L 80 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL L 299 " --> pdb=" O THR L 80 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE L 82 " --> pdb=" O VAL L 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS L 301 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR L 84 " --> pdb=" O CYS L 301 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL L 230 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU L 136 " --> pdb=" O ARG L 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG L 143 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 50 through 52 removed outlier: 7.472A pdb=" N VAL L 11 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE L 52 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS L 13 " --> pdb=" O PHE L 52 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS L 10 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE L 300 " --> pdb=" O LYS L 10 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N MET L 12 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS L 302 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG L 14 " --> pdb=" O CYS L 302 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR L 80 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL L 299 " --> pdb=" O THR L 80 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE L 82 " --> pdb=" O VAL L 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS L 301 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR L 84 " --> pdb=" O CYS L 301 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL L 230 " --> pdb=" O ILE L 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 572 hydrogen bonds defined for protein. 1656 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: 3.48 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2059 1.32 - 1.44: 3155 1.44 - 1.56: 6751 1.56 - 1.69: 20 1.69 - 1.81: 117 Bond restraints: 12102 Sorted by residual: bond pdb=" N ASP K 231 " pdb=" CA ASP K 231 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.27e-02 6.20e+03 8.46e+00 bond pdb=" CG HIS K 191 " pdb=" CD2 HIS K 191 " ideal model delta sigma weight residual 1.354 1.331 0.023 1.10e-02 8.26e+03 4.42e+00 bond pdb=" C5 ADP L1002 " pdb=" C6 ADP L1002 " ideal model delta sigma weight residual 1.490 1.450 0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C4 ADP L1002 " pdb=" C5 ADP L1002 " ideal model delta sigma weight residual 1.490 1.451 0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" N ARG K 190 " pdb=" CA ARG K 190 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.34e-02 5.57e+03 3.80e+00 ... (remaining 12097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 16219 2.32 - 4.63: 147 4.63 - 6.95: 27 6.95 - 9.27: 6 9.27 - 11.58: 5 Bond angle restraints: 16404 Sorted by residual: angle pdb=" CA ASP K 231 " pdb=" CB ASP K 231 " pdb=" CG ASP K 231 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 104.78 116.36 -11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CA ARG K 190 " pdb=" C ARG K 190 " pdb=" O ARG K 190 " ideal model delta sigma weight residual 122.01 118.46 3.55 1.05e+00 9.07e-01 1.15e+01 angle pdb=" C14 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 119.42 109.49 9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C1' ADP L1002 " pdb=" C2' ADP L1002 " pdb=" C3' ADP L1002 " ideal model delta sigma weight residual 111.00 101.14 9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 7188 33.87 - 67.74: 126 67.74 - 101.61: 8 101.61 - 135.49: 17 135.49 - 169.36: 5 Dihedral angle restraints: 7344 sinusoidal: 3032 harmonic: 4312 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.37 -169.36 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -52.60 157.19 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 135.43 138.69 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 7341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1287 0.040 - 0.080: 383 0.080 - 0.119: 130 0.119 - 0.159: 13 0.159 - 0.199: 3 Chirality restraints: 1816 Sorted by residual: chirality pdb=" C3' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C4' GTP A 501 " pdb=" O3' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.67 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" C3' ADP L1002 " pdb=" C2' ADP L1002 " pdb=" C4' ADP L1002 " pdb=" O3' ADP L1002 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" C21 TA1 B 502 " pdb=" C20 TA1 B 502 " pdb=" C24 TA1 B 502 " pdb=" O09 TA1 B 502 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1813 not shown) Planarity restraints: 2114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP L1002 " -0.050 2.00e-02 2.50e+03 2.07e-02 1.18e+01 pdb=" C2 ADP L1002 " -0.000 2.00e-02 2.50e+03 pdb=" C4 ADP L1002 " 0.020 2.00e-02 2.50e+03 pdb=" C5 ADP L1002 " 0.013 2.00e-02 2.50e+03 pdb=" C6 ADP L1002 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP L1002 " 0.007 2.00e-02 2.50e+03 pdb=" N1 ADP L1002 " -0.013 2.00e-02 2.50e+03 pdb=" N3 ADP L1002 " 0.016 2.00e-02 2.50e+03 pdb=" N6 ADP L1002 " -0.015 2.00e-02 2.50e+03 pdb=" N7 ADP L1002 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ADP L1002 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 32 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 325 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.025 5.00e-02 4.00e+02 ... (remaining 2111 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 125 2.59 - 3.17: 9737 3.17 - 3.74: 17885 3.74 - 4.32: 24442 4.32 - 4.90: 41516 Nonbonded interactions: 93705 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.010 2.170 nonbonded pdb=" O TYR L 277 " pdb=" OG1 THR L 283 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR L 92 " pdb="MG MG L1001 " model vdw 2.211 2.170 nonbonded pdb=" O GLY L 90 " pdb=" OG1 THR L 94 " model vdw 2.225 3.040 nonbonded pdb=" OG SER L 175 " pdb=" OD1 ASP L 177 " model vdw 2.230 3.040 ... (remaining 93700 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 'K' and (resid 8 through 236 or resid 255 through 323 or resid 1001)) selection = (chain 'L' and (resid 8 through 64 or (resid 65 through 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 191 or (resid 192 throug \ h 193 and (name N or name CA or name C or name O or name CB )) or resid 194 or r \ esid 199 through 323 or resid 1002)) } 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=0.00 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: 0.950 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.380 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.008 0.814 12103 Z= 0.753 Angle : 0.605 11.583 16404 Z= 0.298 Chirality : 0.043 0.199 1816 Planarity : 0.004 0.055 2114 Dihedral : 15.376 169.357 4572 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1469 helix: 1.55 (0.22), residues: 580 sheet: 0.95 (0.32), residues: 280 loop : -1.34 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS K 191 PHE 0.008 0.001 PHE A 255 TYR 0.008 0.001 TYR A 312 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.17490 ( 517) hydrogen bonds : angle 6.23101 ( 1656) covalent geometry : bond 0.00273 (12102) covalent geometry : angle 0.60472 (16404) Misc. bond : bond 0.81415 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8919 (mmt) cc_final: 0.8624 (mmt) REVERT: B 90 ASP cc_start: 0.8793 (t0) cc_final: 0.8152 (t0) REVERT: B 93 VAL cc_start: 0.9409 (t) cc_final: 0.9175 (m) REVERT: B 124 LYS cc_start: 0.8116 (tptt) cc_final: 0.7657 (ttpt) REVERT: B 197 ASN cc_start: 0.8081 (m-40) cc_final: 0.7875 (m110) REVERT: B 202 TYR cc_start: 0.8806 (m-80) cc_final: 0.8571 (m-80) REVERT: B 282 GLN cc_start: 0.8783 (mp10) cc_final: 0.7608 (mp10) REVERT: B 326 LYS cc_start: 0.8888 (tttm) cc_final: 0.8683 (tmtt) REVERT: A 205 ASP cc_start: 0.8827 (p0) cc_final: 0.8514 (p0) REVERT: A 377 MET cc_start: 0.8057 (ttp) cc_final: 0.7842 (tmm) REVERT: A 390 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8157 (ptp90) REVERT: A 425 MET cc_start: 0.9154 (mmm) cc_final: 0.8486 (tpp) REVERT: L 197 MET cc_start: 0.3078 (tpt) cc_final: 0.2406 (ttt) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.2749 time to fit residues: 116.7752 Evaluate side-chains 160 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 256 GLN K 93 HIS K 160 ASN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN L 196 ASN L 211 ASN L 320 GLN ** L 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.076378 restraints weight = 28142.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078705 restraints weight = 12974.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080232 restraints weight = 7888.372| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12103 Z= 0.182 Angle : 0.646 10.517 16404 Z= 0.322 Chirality : 0.046 0.367 1816 Planarity : 0.004 0.050 2114 Dihedral : 11.708 170.686 1765 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.55 % Allowed : 13.59 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1469 helix: 1.53 (0.22), residues: 597 sheet: 0.99 (0.32), residues: 284 loop : -1.23 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS A 192 PHE 0.020 0.002 PHE L 116 TYR 0.009 0.001 TYR K 274 ARG 0.005 0.001 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 517) hydrogen bonds : angle 4.39466 ( 1656) covalent geometry : bond 0.00411 (12102) covalent geometry : angle 0.64633 (16404) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8646 (t0) cc_final: 0.7962 (t0) REVERT: B 93 VAL cc_start: 0.9354 (t) cc_final: 0.9091 (m) REVERT: B 124 LYS cc_start: 0.7895 (tptt) cc_final: 0.7372 (ttpt) REVERT: A 196 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: A 211 ASP cc_start: 0.9109 (t70) cc_final: 0.8630 (t0) REVERT: A 377 MET cc_start: 0.7860 (ttp) cc_final: 0.7560 (tmm) REVERT: A 390 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7962 (ptp90) REVERT: A 425 MET cc_start: 0.8995 (mmm) cc_final: 0.8445 (tpt) REVERT: K 48 PHE cc_start: 0.8774 (m-80) cc_final: 0.8353 (m-10) REVERT: L 12 MET cc_start: 0.4521 (tpp) cc_final: 0.4115 (mmm) REVERT: L 52 PHE cc_start: 0.1564 (m-80) cc_final: 0.0879 (m-80) REVERT: L 197 MET cc_start: 0.5054 (tpt) cc_final: 0.4014 (ttt) outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.2838 time to fit residues: 81.0535 Evaluate side-chains 170 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 71 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN L 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076010 restraints weight = 28236.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078452 restraints weight = 12968.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080020 restraints weight = 7790.458| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12103 Z= 0.148 Angle : 0.570 6.278 16404 Z= 0.286 Chirality : 0.045 0.348 1816 Planarity : 0.004 0.059 2114 Dihedral : 10.000 166.876 1765 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.01 % Allowed : 14.05 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.22), residues: 1469 helix: 1.61 (0.22), residues: 597 sheet: 1.18 (0.32), residues: 277 loop : -1.17 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS A 192 PHE 0.017 0.001 PHE L 116 TYR 0.008 0.001 TYR K 134 ARG 0.007 0.000 ARG L 321 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 517) hydrogen bonds : angle 4.13146 ( 1656) covalent geometry : bond 0.00335 (12102) covalent geometry : angle 0.56970 (16404) Misc. bond : bond 0.00239 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8716 (t0) cc_final: 0.8078 (t0) REVERT: B 93 VAL cc_start: 0.9330 (t) cc_final: 0.9060 (m) REVERT: A 196 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: A 211 ASP cc_start: 0.9136 (t70) cc_final: 0.8609 (t0) REVERT: A 390 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7999 (ptp90) REVERT: A 425 MET cc_start: 0.8979 (mmm) cc_final: 0.8380 (tpp) REVERT: A 430 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8144 (mmtm) REVERT: K 34 GLN cc_start: 0.7163 (mm110) cc_final: 0.6913 (mm-40) REVERT: K 48 PHE cc_start: 0.8891 (m-80) cc_final: 0.8586 (m-10) REVERT: L 12 MET cc_start: 0.4601 (tpp) cc_final: 0.4186 (mmt) REVERT: L 16 ARG cc_start: -0.0109 (ptt90) cc_final: -0.1133 (ptm160) REVERT: L 52 PHE cc_start: 0.1642 (m-80) cc_final: 0.1117 (m-80) REVERT: L 197 MET cc_start: 0.5200 (tpt) cc_final: 0.4019 (ttt) outliers start: 39 outliers final: 27 residues processed: 180 average time/residue: 0.2300 time to fit residues: 60.6976 Evaluate side-chains 173 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 117 optimal weight: 30.0000 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 HIS K 253 ASN ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.112326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077778 restraints weight = 28241.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.080217 restraints weight = 12851.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081806 restraints weight = 7751.736| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12103 Z= 0.102 Angle : 0.535 5.999 16404 Z= 0.267 Chirality : 0.044 0.267 1816 Planarity : 0.003 0.053 2114 Dihedral : 9.504 160.445 1765 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.78 % Allowed : 14.90 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1469 helix: 1.82 (0.22), residues: 598 sheet: 1.20 (0.32), residues: 282 loop : -1.12 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.002 0.001 HIS B 229 PHE 0.015 0.001 PHE L 318 TYR 0.007 0.001 TYR A 108 ARG 0.003 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 517) hydrogen bonds : angle 3.86439 ( 1656) covalent geometry : bond 0.00218 (12102) covalent geometry : angle 0.53517 (16404) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: B 19 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8754 (tptt) REVERT: B 90 ASP cc_start: 0.8740 (t0) cc_final: 0.8106 (t0) REVERT: B 93 VAL cc_start: 0.9290 (t) cc_final: 0.9050 (m) REVERT: A 71 GLU cc_start: 0.7650 (tt0) cc_final: 0.7386 (tm-30) REVERT: A 161 TYR cc_start: 0.8563 (m-80) cc_final: 0.8295 (m-80) REVERT: A 211 ASP cc_start: 0.9129 (t70) cc_final: 0.8566 (t0) REVERT: A 390 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7982 (ptp90) REVERT: A 425 MET cc_start: 0.9042 (mmm) cc_final: 0.8398 (tpp) REVERT: A 430 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8199 (mmtm) REVERT: K 48 PHE cc_start: 0.8775 (m-80) cc_final: 0.8225 (m-10) REVERT: K 311 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: L 12 MET cc_start: 0.4353 (tpp) cc_final: 0.3919 (mmm) REVERT: L 39 VAL cc_start: 0.4094 (OUTLIER) cc_final: 0.3640 (m) REVERT: L 52 PHE cc_start: 0.1513 (m-80) cc_final: 0.0969 (m-80) REVERT: L 197 MET cc_start: 0.5179 (tpt) cc_final: 0.4066 (ttt) outliers start: 36 outliers final: 23 residues processed: 180 average time/residue: 0.2381 time to fit residues: 62.1759 Evaluate side-chains 167 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075135 restraints weight = 28541.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077445 restraints weight = 13255.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078949 restraints weight = 8062.653| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 12103 Z= 0.178 Angle : 0.582 9.953 16404 Z= 0.292 Chirality : 0.044 0.250 1816 Planarity : 0.004 0.055 2114 Dihedral : 9.315 153.650 1765 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.17 % Allowed : 15.37 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1469 helix: 1.73 (0.22), residues: 597 sheet: 1.18 (0.33), residues: 277 loop : -1.13 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.004 0.001 HIS A 192 PHE 0.011 0.001 PHE B 296 TYR 0.009 0.001 TYR K 274 ARG 0.004 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 517) hydrogen bonds : angle 3.99326 ( 1656) covalent geometry : bond 0.00412 (12102) covalent geometry : angle 0.58216 (16404) Misc. bond : bond 0.00227 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8743 (t0) cc_final: 0.8069 (t0) REVERT: B 124 LYS cc_start: 0.7952 (tptt) cc_final: 0.7437 (ttpt) REVERT: A 161 TYR cc_start: 0.8777 (m-80) cc_final: 0.8476 (m-80) REVERT: A 196 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: A 211 ASP cc_start: 0.9147 (t70) cc_final: 0.8611 (t0) REVERT: A 390 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.8015 (ptp90) REVERT: A 425 MET cc_start: 0.9021 (mmm) cc_final: 0.8374 (tpp) REVERT: A 430 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8228 (mmtm) REVERT: K 48 PHE cc_start: 0.8788 (m-80) cc_final: 0.8522 (m-10) REVERT: K 95 MET cc_start: 0.9109 (mmm) cc_final: 0.8874 (mmm) REVERT: K 311 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: L 12 MET cc_start: 0.4415 (tpp) cc_final: 0.4153 (mmt) REVERT: L 39 VAL cc_start: 0.4044 (OUTLIER) cc_final: 0.3632 (m) REVERT: L 52 PHE cc_start: 0.1680 (m-80) cc_final: 0.1080 (m-80) REVERT: L 197 MET cc_start: 0.5053 (tpt) cc_final: 0.3882 (ttt) outliers start: 41 outliers final: 32 residues processed: 164 average time/residue: 0.2671 time to fit residues: 63.4479 Evaluate side-chains 169 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN A 256 GLN ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076147 restraints weight = 28554.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078558 restraints weight = 13232.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.080093 restraints weight = 8075.302| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12103 Z= 0.115 Angle : 0.545 7.804 16404 Z= 0.270 Chirality : 0.043 0.227 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.914 149.838 1765 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.24 % Allowed : 15.68 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1469 helix: 1.84 (0.22), residues: 598 sheet: 1.16 (0.32), residues: 284 loop : -1.05 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS A 192 PHE 0.015 0.001 PHE L 318 TYR 0.007 0.001 TYR K 274 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 517) hydrogen bonds : angle 3.80292 ( 1656) covalent geometry : bond 0.00258 (12102) covalent geometry : angle 0.54515 (16404) Misc. bond : bond 0.00154 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8759 (t0) cc_final: 0.8122 (t0) REVERT: A 161 TYR cc_start: 0.8696 (m-80) cc_final: 0.8424 (m-80) REVERT: A 211 ASP cc_start: 0.9130 (t70) cc_final: 0.8533 (t0) REVERT: A 390 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7941 (ptp90) REVERT: A 425 MET cc_start: 0.8997 (mmm) cc_final: 0.8489 (tpp) REVERT: A 430 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8258 (mmtm) REVERT: K 95 MET cc_start: 0.9208 (mmm) cc_final: 0.8941 (mmm) REVERT: K 311 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: L 39 VAL cc_start: 0.4356 (OUTLIER) cc_final: 0.3904 (m) REVERT: L 197 MET cc_start: 0.5041 (tpt) cc_final: 0.3985 (ttt) outliers start: 42 outliers final: 31 residues processed: 170 average time/residue: 0.2232 time to fit residues: 55.6361 Evaluate side-chains 167 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 96 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 140 optimal weight: 0.0020 chunk 35 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.111150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076433 restraints weight = 28720.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078895 restraints weight = 13238.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.080452 restraints weight = 7966.858| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12103 Z= 0.113 Angle : 0.551 8.286 16404 Z= 0.272 Chirality : 0.043 0.228 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.672 148.323 1765 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.17 % Allowed : 15.83 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1469 helix: 1.85 (0.22), residues: 599 sheet: 1.17 (0.33), residues: 284 loop : -1.01 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.002 0.000 HIS A 192 PHE 0.008 0.001 PHE A 255 TYR 0.007 0.001 TYR K 274 ARG 0.005 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 517) hydrogen bonds : angle 3.76244 ( 1656) covalent geometry : bond 0.00256 (12102) covalent geometry : angle 0.55124 (16404) Misc. bond : bond 0.00152 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8051 (t0) REVERT: A 161 TYR cc_start: 0.8687 (m-80) cc_final: 0.8455 (m-80) REVERT: A 196 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: A 211 ASP cc_start: 0.9118 (t0) cc_final: 0.8528 (t0) REVERT: A 390 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7929 (ptp90) REVERT: A 425 MET cc_start: 0.8988 (mmm) cc_final: 0.8477 (tpp) REVERT: A 430 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8228 (mmtm) REVERT: K 37 ASP cc_start: 0.8373 (p0) cc_final: 0.8095 (m-30) REVERT: K 311 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: L 32 LYS cc_start: 0.7119 (tptp) cc_final: 0.6646 (mmmt) REVERT: L 39 VAL cc_start: 0.4344 (OUTLIER) cc_final: 0.3893 (m) REVERT: L 129 HIS cc_start: 0.6407 (m-70) cc_final: 0.6058 (m-70) REVERT: L 197 MET cc_start: 0.5089 (tpt) cc_final: 0.4030 (ttt) outliers start: 41 outliers final: 29 residues processed: 170 average time/residue: 0.3240 time to fit residues: 80.6852 Evaluate side-chains 168 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076046 restraints weight = 28922.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078381 restraints weight = 13738.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.079872 restraints weight = 8460.404| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12103 Z= 0.118 Angle : 0.556 8.202 16404 Z= 0.274 Chirality : 0.043 0.220 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.528 147.561 1765 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.01 % Allowed : 16.37 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1469 helix: 1.87 (0.22), residues: 598 sheet: 1.21 (0.33), residues: 283 loop : -0.99 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.002 0.000 HIS A 192 PHE 0.017 0.001 PHE L 318 TYR 0.008 0.001 TYR K 274 ARG 0.005 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 517) hydrogen bonds : angle 3.76862 ( 1656) covalent geometry : bond 0.00271 (12102) covalent geometry : angle 0.55570 (16404) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8674 (t0) cc_final: 0.8038 (t0) REVERT: B 124 LYS cc_start: 0.7947 (tptt) cc_final: 0.7480 (ttpt) REVERT: B 137 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 161 TYR cc_start: 0.8706 (m-80) cc_final: 0.8477 (m-80) REVERT: A 196 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: A 211 ASP cc_start: 0.9134 (t0) cc_final: 0.8547 (t0) REVERT: A 390 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7942 (mtm180) REVERT: A 425 MET cc_start: 0.8970 (mmm) cc_final: 0.8405 (tpp) REVERT: A 430 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8307 (mmtm) REVERT: K 37 ASP cc_start: 0.8426 (p0) cc_final: 0.8122 (m-30) REVERT: K 95 MET cc_start: 0.9125 (mmm) cc_final: 0.8721 (mmm) REVERT: K 131 LYS cc_start: 0.8037 (mttp) cc_final: 0.7793 (mttp) REVERT: K 311 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: L 12 MET cc_start: 0.6021 (mmp) cc_final: 0.4405 (mmm) REVERT: L 30 ILE cc_start: 0.4870 (pt) cc_final: 0.3737 (mm) REVERT: L 32 LYS cc_start: 0.7130 (tptp) cc_final: 0.6665 (mmmt) REVERT: L 39 VAL cc_start: 0.4344 (OUTLIER) cc_final: 0.3886 (m) REVERT: L 95 MET cc_start: 0.6600 (tpp) cc_final: 0.5702 (ptm) REVERT: L 129 HIS cc_start: 0.6386 (m-70) cc_final: 0.5984 (m-70) REVERT: L 197 MET cc_start: 0.5087 (tpt) cc_final: 0.4029 (ttt) outliers start: 39 outliers final: 30 residues processed: 169 average time/residue: 0.2861 time to fit residues: 70.8900 Evaluate side-chains 169 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.076953 restraints weight = 28534.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079277 restraints weight = 13571.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080778 restraints weight = 8332.921| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12103 Z= 0.106 Angle : 0.552 8.052 16404 Z= 0.271 Chirality : 0.043 0.215 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.341 146.638 1765 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.78 % Allowed : 16.68 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.03 (0.23), residues: 1469 helix: 1.91 (0.22), residues: 598 sheet: 1.30 (0.33), residues: 281 loop : -0.95 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.002 0.000 HIS A 406 PHE 0.009 0.001 PHE B 418 TYR 0.007 0.001 TYR K 274 ARG 0.002 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 517) hydrogen bonds : angle 3.71221 ( 1656) covalent geometry : bond 0.00239 (12102) covalent geometry : angle 0.55188 (16404) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8680 (t0) cc_final: 0.8044 (t0) REVERT: B 124 LYS cc_start: 0.7938 (tptt) cc_final: 0.7570 (tttt) REVERT: B 137 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 161 TYR cc_start: 0.8672 (m-80) cc_final: 0.8448 (m-80) REVERT: A 196 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: A 211 ASP cc_start: 0.9127 (t0) cc_final: 0.8535 (t0) REVERT: A 390 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7940 (ptp90) REVERT: A 430 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8279 (mmtm) REVERT: K 37 ASP cc_start: 0.8383 (p0) cc_final: 0.8109 (m-30) REVERT: K 95 MET cc_start: 0.9176 (mmm) cc_final: 0.8796 (mmm) REVERT: K 117 ASN cc_start: 0.8814 (m-40) cc_final: 0.8530 (t0) REVERT: K 311 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8247 (pt0) REVERT: L 12 MET cc_start: 0.5994 (mmp) cc_final: 0.4443 (mmm) REVERT: L 30 ILE cc_start: 0.4500 (pt) cc_final: 0.3427 (mm) REVERT: L 32 LYS cc_start: 0.7203 (tptp) cc_final: 0.6714 (mmmt) REVERT: L 39 VAL cc_start: 0.4501 (OUTLIER) cc_final: 0.4025 (m) REVERT: L 129 HIS cc_start: 0.6349 (m-70) cc_final: 0.5971 (m-70) REVERT: L 197 MET cc_start: 0.5140 (tpt) cc_final: 0.4058 (ttt) outliers start: 36 outliers final: 28 residues processed: 168 average time/residue: 0.3226 time to fit residues: 82.2172 Evaluate side-chains 171 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 263 ASN Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 85 optimal weight: 0.0050 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078043 restraints weight = 28059.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080456 restraints weight = 12922.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082027 restraints weight = 7783.725| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12103 Z= 0.098 Angle : 0.553 7.730 16404 Z= 0.270 Chirality : 0.043 0.203 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.195 146.263 1765 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.55 % Allowed : 17.14 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.23), residues: 1469 helix: 1.92 (0.22), residues: 595 sheet: 1.31 (0.33), residues: 283 loop : -0.92 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.002 0.000 HIS A 406 PHE 0.012 0.001 PHE L 318 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 517) hydrogen bonds : angle 3.70044 ( 1656) covalent geometry : bond 0.00219 (12102) covalent geometry : angle 0.55277 (16404) Misc. bond : bond 0.00119 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8691 (t0) cc_final: 0.8058 (t0) REVERT: B 124 LYS cc_start: 0.7916 (tptt) cc_final: 0.7517 (tttt) REVERT: B 137 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8483 (tt) REVERT: A 196 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: A 211 ASP cc_start: 0.9123 (t0) cc_final: 0.8542 (t0) REVERT: A 430 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8333 (mmtm) REVERT: K 37 ASP cc_start: 0.8432 (p0) cc_final: 0.8130 (m-30) REVERT: K 95 MET cc_start: 0.9200 (mmm) cc_final: 0.8825 (mmm) REVERT: K 117 ASN cc_start: 0.8803 (m-40) cc_final: 0.8534 (t0) REVERT: K 311 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: L 12 MET cc_start: 0.6012 (mmp) cc_final: 0.4271 (mmm) REVERT: L 30 ILE cc_start: 0.4484 (pt) cc_final: 0.3511 (mm) REVERT: L 32 LYS cc_start: 0.7382 (tptp) cc_final: 0.6893 (mmmt) REVERT: L 39 VAL cc_start: 0.4428 (OUTLIER) cc_final: 0.3941 (m) REVERT: L 52 PHE cc_start: 0.1983 (m-80) cc_final: 0.1582 (m-80) REVERT: L 129 HIS cc_start: 0.6348 (m-70) cc_final: 0.5973 (m-70) REVERT: L 197 MET cc_start: 0.5233 (tpt) cc_final: 0.4206 (ttt) REVERT: L 318 PHE cc_start: 0.5540 (m-80) cc_final: 0.4524 (m-10) outliers start: 33 outliers final: 27 residues processed: 166 average time/residue: 0.2768 time to fit residues: 66.9139 Evaluate side-chains 169 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 311 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 278 ARG Chi-restraints excluded: chain L residue 306 SER Chi-restraints excluded: chain L residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.074730 restraints weight = 29034.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077022 restraints weight = 13832.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078542 restraints weight = 8530.804| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 12103 Z= 0.190 Angle : 0.614 8.625 16404 Z= 0.308 Chirality : 0.045 0.219 1816 Planarity : 0.004 0.054 2114 Dihedral : 8.348 142.636 1765 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.86 % Allowed : 16.99 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1469 helix: 1.71 (0.22), residues: 600 sheet: 1.10 (0.32), residues: 284 loop : -0.92 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 21 HIS 0.005 0.001 HIS A 192 PHE 0.016 0.001 PHE L 318 TYR 0.011 0.001 TYR K 274 ARG 0.004 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 517) hydrogen bonds : angle 3.98125 ( 1656) covalent geometry : bond 0.00439 (12102) covalent geometry : angle 0.61397 (16404) Misc. bond : bond 0.00231 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.47 seconds wall clock time: 102 minutes 19.77 seconds (6139.77 seconds total)