Starting phenix.real_space_refine on Sat Jan 18 05:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8riz_19192/01_2025/8riz_19192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8riz_19192/01_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_19192/01_2025/8riz_19192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8riz_19192/01_2025/8riz_19192.map" model { file = "/net/cci-nas-00/data/ceres_data/8riz_19192/01_2025/8riz_19192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8riz_19192/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.35, per 1000 atoms: 0.62 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 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: 1.39 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: 3.94 Time building geometry restraints manager: 3.46 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: 0.650 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.320 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- 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 : 0.003 0.040 12102 Z= 0.179 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 *********************** 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 : 1.301 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: 0.2912 time to fit residues: 124.1631 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 : 1.581 ------------------------------------------------------------------------------- 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 = 28142.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078705 restraints weight = 12984.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080218 restraints weight = 7890.298| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 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 = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- 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 12102 Z= 0.266 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 *********************** 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 : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8645 (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: 0.7395 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: A 211 ASP cc_start: 0.9108 (t70) cc_final: 0.8629 (t0) REVERT: A 377 MET cc_start: 0.7860 (ttp) cc_final: 0.7561 (tmm) REVERT: A 390 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7962 (ptp90) REVERT: A 425 MET cc_start: 0.8993 (mmm) cc_final: 0.8443 (tpt) REVERT: K 48 PHE cc_start: 0.8774 (m-80) cc_final: 0.8354 (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: 0.0880 (m-80) REVERT: L 197 MET cc_start: 0.5058 (tpt) cc_final: 0.4019 (ttt) outliers start: 33 outliers final: 21 residues processed: 197 average time/residue: 0.2572 time to fit residues: 71.9571 Evaluate side-chains 169 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.111842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077249 restraints weight = 28054.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079705 restraints weight = 12780.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081312 restraints weight = 7668.488| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12102 Z= 0.168 Angle : 0.554 6.215 16404 Z= 0.278 Chirality : 0.044 0.341 1816 Planarity : 0.004 0.056 2114 Dihedral : 9.949 166.954 1765 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.70 % Allowed : 14.44 % Favored : 82.86 % 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: 0.75 (0.22), residues: 1469 helix: 1.68 (0.22), residues: 597 sheet: 1.21 (0.32), residues: 277 loop : -1.12 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS L 129 PHE 0.016 0.001 PHE L 116 TYR 0.007 0.001 TYR K 134 ARG 0.007 0.000 ARG L 321 *********************** 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 200 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8683 (t0) cc_final: 0.8046 (t0) REVERT: B 93 VAL cc_start: 0.9343 (t) cc_final: 0.9091 (m) REVERT: A 196 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: A 211 ASP cc_start: 0.9136 (t70) cc_final: 0.8618 (t0) REVERT: A 390 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7974 (ptp90) REVERT: A 425 MET cc_start: 0.9015 (mmm) cc_final: 0.8432 (tpp) REVERT: A 430 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8171 (mmtm) REVERT: K 34 GLN cc_start: 0.7106 (mm110) cc_final: 0.6875 (mm-40) REVERT: K 48 PHE cc_start: 0.8862 (m-80) cc_final: 0.8538 (m-10) REVERT: L 12 MET cc_start: 0.4469 (tpp) cc_final: 0.3967 (mmm) REVERT: L 52 PHE cc_start: 0.1550 (m-80) cc_final: 0.1025 (m-80) REVERT: L 197 MET cc_start: 0.5177 (tpt) cc_final: 0.4005 (ttt) REVERT: L 320 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6184 (mm-40) outliers start: 35 outliers final: 23 residues processed: 188 average time/residue: 0.2328 time to fit residues: 63.9795 Evaluate side-chains 174 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 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 320 GLN 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: 0.4980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 30.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078016 restraints weight = 28200.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080512 restraints weight = 12753.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082146 restraints weight = 7627.843| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 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 = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12102 Z= 0.139 Angle : 0.537 6.120 16404 Z= 0.268 Chirality : 0.043 0.284 1816 Planarity : 0.003 0.053 2114 Dihedral : 9.604 161.760 1765 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.55 % Allowed : 15.21 % Favored : 82.24 % 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 (0.22), residues: 1469 helix: 1.77 (0.22), residues: 597 sheet: 1.22 (0.32), residues: 282 loop : -1.06 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.002 0.000 HIS B 229 PHE 0.019 0.001 PHE L 318 TYR 0.006 0.001 TYR A 108 ARG 0.004 0.000 ARG B 308 *********************** 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 185 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 90 ASP cc_start: 0.8748 (t0) cc_final: 0.8133 (t0) REVERT: B 93 VAL cc_start: 0.9330 (t) cc_final: 0.9091 (m) REVERT: A 71 GLU cc_start: 0.7607 (tt0) cc_final: 0.7319 (tm-30) REVERT: A 211 ASP cc_start: 0.9128 (t70) cc_final: 0.8566 (t0) REVERT: A 390 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7944 (ptp90) REVERT: A 425 MET cc_start: 0.9036 (mmm) cc_final: 0.8381 (tpp) REVERT: A 430 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8206 (mmtm) REVERT: K 48 PHE cc_start: 0.8767 (m-80) cc_final: 0.8451 (m-10) REVERT: K 311 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: L 52 PHE cc_start: 0.1614 (m-80) cc_final: 0.1126 (m-80) REVERT: L 197 MET cc_start: 0.5183 (tpt) cc_final: 0.4078 (ttt) outliers start: 33 outliers final: 25 residues processed: 173 average time/residue: 0.2318 time to fit residues: 59.2228 Evaluate side-chains 168 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 195 VAL Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 234 THR 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 344 VAL 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 273 THR 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 16 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.107232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073124 restraints weight = 28800.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075319 restraints weight = 13993.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076765 restraints weight = 8722.783| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 12102 Z= 0.443 Angle : 0.671 9.740 16404 Z= 0.341 Chirality : 0.047 0.272 1816 Planarity : 0.004 0.052 2114 Dihedral : 9.595 154.935 1765 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.02 % Allowed : 14.75 % Favored : 81.24 % 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: 0.48 (0.22), residues: 1469 helix: 1.39 (0.21), residues: 599 sheet: 1.00 (0.32), residues: 277 loop : -1.16 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 388 HIS 0.007 0.001 HIS A 192 PHE 0.014 0.002 PHE A 395 TYR 0.014 0.002 TYR L 138 ARG 0.004 0.000 ARG K 110 *********************** 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 187 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: B 124 LYS cc_start: 0.7946 (tptt) cc_final: 0.7461 (ttpt) REVERT: A 196 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: A 390 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.8061 (ptp90) REVERT: A 425 MET cc_start: 0.8981 (mmm) cc_final: 0.8361 (tpp) REVERT: A 430 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8340 (mmtm) REVERT: K 48 PHE cc_start: 0.8902 (m-80) cc_final: 0.8386 (m-10) REVERT: K 311 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: L 39 VAL cc_start: 0.4083 (OUTLIER) cc_final: 0.3707 (m) REVERT: L 197 MET cc_start: 0.4954 (tpt) cc_final: 0.3711 (ttt) outliers start: 52 outliers final: 42 residues processed: 170 average time/residue: 0.2438 time to fit residues: 60.8420 Evaluate side-chains 171 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 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 9 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 190 THR 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 322 ASP 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 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 K residue 311 GLU Chi-restraints excluded: chain L residue 16 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.3444 ------------------------------------------------------------------------------- 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** 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 = 0.3677 r_free = 0.3677 target = 0.108954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074193 restraints weight = 28738.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.076537 restraints weight = 13491.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078033 restraints weight = 8251.233| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 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 = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12102 Z= 0.203 Angle : 0.574 6.111 16404 Z= 0.288 Chirality : 0.044 0.237 1816 Planarity : 0.004 0.055 2114 Dihedral : 9.174 151.921 1765 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.32 % Allowed : 16.06 % 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: 0.68 (0.22), residues: 1469 helix: 1.65 (0.22), residues: 599 sheet: 0.97 (0.32), residues: 276 loop : -1.07 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS A 192 PHE 0.009 0.001 PHE L 208 TYR 0.008 0.001 TYR K 274 ARG 0.003 0.000 ARG B 308 *********************** 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 179 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: B 19 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8742 (tptt) REVERT: A 196 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: A 390 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7993 (ptp90) REVERT: A 425 MET cc_start: 0.9025 (mmm) cc_final: 0.8459 (tpp) REVERT: A 430 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8253 (mmtm) REVERT: K 48 PHE cc_start: 0.8849 (m-80) cc_final: 0.8324 (m-10) REVERT: K 311 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: L 197 MET cc_start: 0.5190 (tpt) cc_final: 0.4138 (ttt) outliers start: 43 outliers final: 32 residues processed: 166 average time/residue: 0.2408 time to fit residues: 58.1606 Evaluate side-chains 162 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 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 218 ASP Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 322 ASP 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 16 ARG 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: 10.0000 chunk 142 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.108065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073836 restraints weight = 28904.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.076162 restraints weight = 13405.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077673 restraints weight = 8147.728| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12102 Z= 0.268 Angle : 0.596 9.758 16404 Z= 0.298 Chirality : 0.044 0.240 1816 Planarity : 0.004 0.054 2114 Dihedral : 8.980 150.798 1765 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.71 % Allowed : 15.68 % 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: 0.64 (0.22), residues: 1469 helix: 1.60 (0.22), residues: 601 sheet: 0.91 (0.32), residues: 277 loop : -1.07 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.005 0.001 HIS A 192 PHE 0.020 0.001 PHE L 318 TYR 0.010 0.001 TYR K 274 ARG 0.005 0.000 ARG B 308 *********************** 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 174 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: B 19 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8752 (tptt) REVERT: B 137 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 196 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: A 390 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.8019 (ptp90) REVERT: A 425 MET cc_start: 0.9023 (mmm) cc_final: 0.8728 (tpt) REVERT: A 430 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8270 (mmtm) REVERT: K 95 MET cc_start: 0.9190 (mmm) cc_final: 0.8809 (mmm) REVERT: K 311 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: L 12 MET cc_start: 0.6034 (mmp) cc_final: 0.4838 (mmp) REVERT: L 39 VAL cc_start: 0.4540 (OUTLIER) cc_final: 0.4092 (m) REVERT: L 197 MET cc_start: 0.5033 (tpt) cc_final: 0.3900 (ttt) outliers start: 48 outliers final: 36 residues processed: 160 average time/residue: 0.2531 time to fit residues: 59.0058 Evaluate side-chains 164 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 74 THR 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 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 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 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 147 SER 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 376 CYS 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 16 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 84 optimal weight: 8.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- 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** B 336 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 = 0.3694 r_free = 0.3694 target = 0.109794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075705 restraints weight = 29140.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078072 restraints weight = 13656.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079568 restraints weight = 8252.420| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12102 Z= 0.165 Angle : 0.558 6.897 16404 Z= 0.277 Chirality : 0.043 0.219 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.631 150.175 1765 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.78 % Allowed : 16.83 % Favored : 80.39 % 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: 0.83 (0.23), residues: 1469 helix: 1.82 (0.22), residues: 595 sheet: 1.04 (0.33), residues: 276 loop : -1.03 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 192 PHE 0.019 0.001 PHE L 318 TYR 0.007 0.001 TYR K 274 ARG 0.003 0.000 ARG B 308 *********************** 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 172 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7933 (ptp90) REVERT: A 425 MET cc_start: 0.8988 (mmm) cc_final: 0.8478 (tpp) REVERT: A 430 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8261 (mmtm) REVERT: K 37 ASP cc_start: 0.8454 (p0) cc_final: 0.8168 (m-30) REVERT: K 95 MET cc_start: 0.9174 (mmm) cc_final: 0.8783 (mmm) REVERT: K 117 ASN cc_start: 0.8826 (m-40) cc_final: 0.8515 (t0) REVERT: K 311 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: L 12 MET cc_start: 0.5959 (mmp) cc_final: 0.4727 (mmp) REVERT: L 32 LYS cc_start: 0.7263 (tptp) cc_final: 0.6790 (mmmt) REVERT: L 39 VAL cc_start: 0.4481 (OUTLIER) cc_final: 0.4015 (m) REVERT: L 129 HIS cc_start: 0.6367 (m-70) cc_final: 0.5875 (m90) REVERT: L 197 MET cc_start: 0.5150 (tpt) cc_final: 0.4072 (ttt) outliers start: 36 outliers final: 28 residues processed: 159 average time/residue: 0.2697 time to fit residues: 60.9597 Evaluate side-chains 160 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 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 A residue 1 MET Chi-restraints excluded: chain A residue 2 ARG 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 257 THR 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 16 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 94 optimal weight: 0.0870 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** 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 = 0.3692 r_free = 0.3692 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.075395 restraints weight = 28677.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077737 restraints weight = 13608.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.079248 restraints weight = 8356.258| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12102 Z= 0.181 Angle : 0.570 6.917 16404 Z= 0.282 Chirality : 0.043 0.217 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.495 149.042 1765 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.09 % Allowed : 16.45 % Favored : 80.46 % 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: 0.81 (0.23), residues: 1469 helix: 1.76 (0.22), residues: 600 sheet: 0.99 (0.33), residues: 283 loop : -1.02 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS A 192 PHE 0.008 0.001 PHE L 208 TYR 0.008 0.001 TYR K 274 ARG 0.003 0.000 ARG B 308 *********************** 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 174 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: B 137 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8469 (tt) REVERT: A 196 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: A 425 MET cc_start: 0.8977 (mmm) cc_final: 0.8418 (tpp) REVERT: A 430 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8236 (mmtm) REVERT: K 37 ASP cc_start: 0.8358 (p0) cc_final: 0.8135 (m-30) REVERT: K 95 MET cc_start: 0.9156 (mmm) cc_final: 0.8769 (mmm) REVERT: K 117 ASN cc_start: 0.8807 (m-40) cc_final: 0.8517 (t0) REVERT: K 311 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: L 12 MET cc_start: 0.6037 (mmp) cc_final: 0.4813 (mmp) REVERT: L 32 LYS cc_start: 0.7251 (tptp) cc_final: 0.6783 (mmmt) REVERT: L 39 VAL cc_start: 0.4692 (OUTLIER) cc_final: 0.4228 (m) REVERT: L 129 HIS cc_start: 0.6363 (m-70) cc_final: 0.5885 (m90) REVERT: L 197 MET cc_start: 0.5152 (tpt) cc_final: 0.4094 (ttt) REVERT: L 318 PHE cc_start: 0.5019 (t80) cc_final: 0.4533 (t80) outliers start: 40 outliers final: 30 residues processed: 164 average time/residue: 0.2509 time to fit residues: 59.7246 Evaluate side-chains 163 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR 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 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 238 VAL 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 257 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 376 CYS 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 16 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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 = 0.3707 r_free = 0.3707 target = 0.110605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076405 restraints weight = 28237.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078706 restraints weight = 13458.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080173 restraints weight = 8286.360| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12102 Z= 0.162 Angle : 0.568 7.300 16404 Z= 0.281 Chirality : 0.043 0.206 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.364 148.294 1765 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.78 % Allowed : 16.91 % 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: 0.85 (0.23), residues: 1469 helix: 1.80 (0.22), residues: 599 sheet: 1.06 (0.33), residues: 280 loop : -1.01 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.002 0.000 HIS A 192 PHE 0.008 0.001 PHE L 208 TYR 0.009 0.001 TYR L 274 ARG 0.004 0.000 ARG A 390 ********************** 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 169 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: B 137 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8389 (tt) REVERT: B 419 THR cc_start: 0.9284 (m) cc_final: 0.9023 (p) REVERT: A 155 GLU cc_start: 0.8168 (pp20) cc_final: 0.7700 (pt0) REVERT: A 196 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: A 430 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8284 (mmtm) REVERT: K 95 MET cc_start: 0.9176 (mmm) cc_final: 0.8848 (mmm) REVERT: K 117 ASN cc_start: 0.8805 (m-40) cc_final: 0.8515 (t0) REVERT: K 131 LYS cc_start: 0.7913 (mttp) cc_final: 0.7690 (mttp) REVERT: L 12 MET cc_start: 0.6053 (mmp) cc_final: 0.4829 (mmp) REVERT: L 32 LYS cc_start: 0.7363 (tptp) cc_final: 0.6923 (mmmt) REVERT: L 39 VAL cc_start: 0.4675 (OUTLIER) cc_final: 0.4211 (m) REVERT: L 129 HIS cc_start: 0.6327 (m-70) cc_final: 0.5973 (m-70) REVERT: L 197 MET cc_start: 0.5218 (tpt) cc_final: 0.4155 (ttt) REVERT: L 318 PHE cc_start: 0.5170 (t80) cc_final: 0.4722 (t80) outliers start: 36 outliers final: 29 residues processed: 159 average time/residue: 0.2614 time to fit residues: 59.7931 Evaluate side-chains 161 residues out of total 1289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR 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 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 257 THR 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 L residue 16 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** B 336 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 = 0.3704 r_free = 0.3704 target = 0.110455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.075727 restraints weight = 28725.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078142 restraints weight = 13453.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.079729 restraints weight = 8168.932| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12102 Z= 0.159 Angle : 0.566 7.212 16404 Z= 0.280 Chirality : 0.043 0.209 1816 Planarity : 0.003 0.055 2114 Dihedral : 8.262 147.845 1765 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.86 % Allowed : 17.07 % Favored : 80.08 % 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: 0.87 (0.23), residues: 1469 helix: 1.81 (0.22), residues: 600 sheet: 1.08 (0.33), residues: 279 loop : -0.99 (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 B 139 PHE 0.008 0.001 PHE B 377 TYR 0.008 0.001 TYR K 274 ARG 0.003 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4188.51 seconds wall clock time: 76 minutes 18.75 seconds (4578.75 seconds total)