Starting phenix.real_space_refine on Wed Sep 17 23:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhh_19176/09_2025/8rhh_19176.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 11 5.49 5 Mg 3 5.21 5 S 79 5.16 5 C 7681 2.51 5 N 2091 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12261 Number of models: 1 Model: "" Number of chains: 11 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: "K" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2710 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 8, 'TRANS': 335} Chain: "L" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2517 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 8, 'TRANS': 308} Chain breaks: 2 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: "T" Number of atoms: 69 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "t" Number of atoms: 69 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} 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: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AALA T 918 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA T 918 " occ=0.50 residue: pdb=" N AGLN T 919 " occ=0.50 ... (7 atoms not shown) pdb=" NE2AGLN T 919 " occ=0.50 residue: pdb=" N AILE T 920 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE T 920 " occ=0.50 residue: pdb=" N AALA T 921 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA T 921 " occ=0.50 residue: pdb=" N ALYS T 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS T 922 " occ=0.50 residue: pdb=" N APRO T 923 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO T 923 " occ=0.50 residue: pdb=" N AILE T 924 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE T 924 " occ=0.50 residue: pdb=" N AARG T 925 " occ=0.50 ... (9 atoms not shown) pdb=" NH2AARG T 925 " occ=0.50 residue: pdb=" N APRO T 926 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO T 926 " occ=0.50 residue: pdb=" N BALA t 918 " occ=0.50 ... (3 atoms not shown) pdb=" CB BALA t 918 " occ=0.50 residue: pdb=" N BGLN t 919 " occ=0.50 ... (7 atoms not shown) pdb=" NE2BGLN t 919 " occ=0.50 residue: pdb=" N BILE t 920 " occ=0.50 ... (6 atoms not shown) pdb=" CD1BILE t 920 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 3.59, per 1000 atoms: 0.29 Number of scatterers: 12261 At special positions: 0 Unit cell: (94.221, 132.126, 141.873, 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 79 16.00 P 11 15.00 Mg 3 11.99 O 2396 8.00 N 2091 7.00 C 7681 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: 1.34 Conformation dependent library (CDL) restraints added in 681.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 45.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.919A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.356A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 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 108 Processing helix chain 'B' and resid 109 through 128 removed outlier: 4.050A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.939A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.519A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) 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 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.548A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.591A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 57 through 66 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.813A pdb=" N VAL K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS K 71 " --> pdb=" O LYS K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 Processing helix chain 'K' and resid 106 through 121 removed outlier: 3.594A pdb=" N ARG K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 190 removed outlier: 3.588A pdb=" N VAL K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'K' and resid 245 through 271 Processing helix chain 'K' and resid 276 through 279 removed outlier: 4.018A pdb=" N ASP K 279 " --> pdb=" O PRO K 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 276 through 279' Processing helix chain 'K' and resid 280 through 286 Processing helix chain 'K' and resid 286 through 292 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 325 removed outlier: 3.958A pdb=" N THR K 324 " --> pdb=" O GLN K 320 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE K 325 " --> pdb=" O ARG K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 346 Processing helix chain 'L' and resid 19 through 26 Processing helix chain 'L' and resid 57 through 76 removed outlier: 4.722A pdb=" N LYS L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE L 69 " --> pdb=" O CYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 121 Processing helix chain 'L' and resid 175 through 189 Processing helix chain 'L' and resid 256 through 271 Processing helix chain 'L' and resid 286 through 292 Processing helix chain 'L' and resid 308 through 323 removed outlier: 3.560A pdb=" N LYS L 313 " --> pdb=" O GLU L 309 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER L 314 " --> pdb=" O SER L 310 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR L 315 " --> pdb=" O GLU L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 346 removed outlier: 3.614A pdb=" N LYS L 346 " --> pdb=" O LYS L 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.706A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.594A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.538A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 5.150A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.515A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.765A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.064A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.669A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.113A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.005A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.632A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 5 through 8 removed outlier: 4.073A pdb=" N ALA K 5 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL K 329 " --> pdb=" O ALA K 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 15 removed outlier: 6.449A pdb=" N CYS K 13 " --> pdb=" O PHE K 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 51 through 52 current: chain 'K' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 141 through 144 current: chain 'K' and resid 222 through 231 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.780A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 154 through 157 removed outlier: 4.341A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AA8, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 15 removed outlier: 4.160A pdb=" N ARG L 50 " --> pdb=" O VAL L 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 50 through 51 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 221 through 229 Processing sheet with id=AB1, first strand: chain 'L' and resid 32 through 33 removed outlier: 3.768A pdb=" N ILE L 41 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 155 through 157 removed outlier: 3.641A pdb=" N TYR L 164 " --> pdb=" O HIS L 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.015A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'A' and resid 269 through 273 No H-bonds generated for sheet with id=AB5 473 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.72 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: 2125 1.32 - 1.44: 3243 1.44 - 1.56: 6997 1.56 - 1.69: 22 1.69 - 1.81: 120 Bond restraints: 12507 Sorted by residual: bond pdb=" O3A ANP K1001 " pdb=" PB ANP K1001 " ideal model delta sigma weight residual 1.700 1.525 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" O3A ANP L1002 " pdb=" PB ANP L1002 " ideal model delta sigma weight residual 1.700 1.530 0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" O5' ANP L1002 " pdb=" PA ANP L1002 " ideal model delta sigma weight residual 1.655 1.514 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 1.795 1.669 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" O5' ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 1.655 1.539 0.116 2.00e-02 2.50e+03 3.35e+01 ... (remaining 12502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 16893 4.35 - 8.69: 44 8.69 - 13.04: 11 13.04 - 17.39: 2 17.39 - 21.73: 1 Bond angle restraints: 16951 Sorted by residual: angle pdb=" C5' ANP K1001 " pdb=" O5' ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 120.74 99.01 21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C3' ANP K1001 " pdb=" C4' ANP K1001 " pdb=" C5' ANP K1001 " ideal model delta sigma weight residual 116.03 99.94 16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O2A ANP L1002 " pdb=" PA ANP L1002 " pdb=" O5' ANP L1002 " ideal model delta sigma weight residual 108.82 92.96 15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O1A ANP L1002 " pdb=" PA ANP L1002 " pdb=" O5' ANP L1002 " ideal model delta sigma weight residual 105.07 92.27 12.80 3.00e+00 1.11e-01 1.82e+01 angle pdb=" PB ANP K1001 " pdb=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 126.95 114.40 12.55 3.00e+00 1.11e-01 1.75e+01 ... (remaining 16946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 7435 34.88 - 69.77: 167 69.77 - 104.65: 17 104.65 - 139.53: 17 139.53 - 174.42: 5 Dihedral angle restraints: 7641 sinusoidal: 3189 harmonic: 4452 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 -120.86 -169.87 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 -52.63 157.23 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 274.12 135.18 138.94 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 7638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1646 0.065 - 0.130: 216 0.130 - 0.195: 7 0.195 - 0.260: 2 0.260 - 0.326: 3 Chirality restraints: 1874 Sorted by residual: chirality pdb=" C4' ANP K1001 " pdb=" C3' ANP K1001 " pdb=" C5' ANP K1001 " pdb=" O4' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.45 -2.78 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' ANP K1001 " pdb=" C2' ANP K1001 " pdb=" C4' ANP K1001 " pdb=" O3' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.03 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' ANP L1002 " pdb=" C2' ANP L1002 " pdb=" C4' ANP L1002 " pdb=" O3' ANP L1002 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1871 not shown) Planarity restraints: 2179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP K1001 " 0.043 2.00e-02 2.50e+03 2.08e-02 1.19e+01 pdb=" C2 ANP K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ANP K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C5 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" C6 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" C8 ANP K1001 " 0.001 2.00e-02 2.50e+03 pdb=" N1 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ANP K1001 " -0.005 2.00e-02 2.50e+03 pdb=" N6 ANP K1001 " 0.012 2.00e-02 2.50e+03 pdb=" N7 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" N9 ANP K1001 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 162 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO K 163 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO K 163 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 162 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C VAL K 162 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL K 162 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO K 163 " 0.009 2.00e-02 2.50e+03 ... (remaining 2176 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 83 2.53 - 3.12: 9164 3.12 - 3.71: 19258 3.71 - 4.31: 27142 4.31 - 4.90: 45720 Nonbonded interactions: 101367 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.931 2.170 nonbonded pdb="MG MG L1001 " pdb=" O2G ANP L1002 " model vdw 1.960 2.170 nonbonded pdb="MG MG L1001 " pdb=" O1B ANP L1002 " model vdw 1.967 2.170 nonbonded pdb=" O3G ANP K1001 " pdb="MG MG K1002 " model vdw 1.984 2.170 nonbonded pdb=" O2B ANP K1001 " pdb="MG MG K1002 " model vdw 2.073 2.170 ... (remaining 101362 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 4 through 191 or resid 202 through 237 or resid 254 throug \ h 346)) selection = (chain 'L' and resid 4 through 346) } ncs_group { reference = chain 'T' selection = chain 't' } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.009 0.842 12508 Z= 0.789 Angle : 0.701 21.735 16951 Z= 0.319 Chirality : 0.045 0.326 1874 Planarity : 0.004 0.054 2179 Dihedral : 16.967 174.417 4777 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.15 % Allowed : 10.84 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.21), residues: 1515 helix: 1.32 (0.21), residues: 599 sheet: 0.00 (0.34), residues: 256 loop : -0.97 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 14 TYR 0.012 0.001 TYR K 29 PHE 0.016 0.001 PHE K 82 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00499 (12507) covalent geometry : angle 0.70067 (16951) hydrogen bonds : bond 0.16359 ( 473) hydrogen bonds : angle 6.07826 ( 1386) Misc. bond : bond 0.84153 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7797 (p0) cc_final: 0.7575 (p0) REVERT: K 9 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (mm) REVERT: K 180 MET cc_start: 0.8824 (mmp) cc_final: 0.8576 (mmp) REVERT: K 335 LEU cc_start: 0.8680 (mt) cc_final: 0.8089 (mm) outliers start: 2 outliers final: 3 residues processed: 366 average time/residue: 0.6601 time to fit residues: 259.7261 Evaluate side-chains 195 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain K residue 9 ILE Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 238 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B 59 ASN B 249 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062993 restraints weight = 28536.714| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.45 r_work: 0.2740 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12508 Z= 0.319 Angle : 0.757 12.372 16951 Z= 0.376 Chirality : 0.048 0.336 1874 Planarity : 0.005 0.050 2179 Dihedral : 14.519 177.518 1866 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.63 % Allowed : 18.68 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1515 helix: 1.43 (0.21), residues: 602 sheet: 0.12 (0.34), residues: 243 loop : -0.75 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 308 TYR 0.024 0.002 TYR L 274 PHE 0.022 0.002 PHE L 318 TRP 0.014 0.002 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00722 (12507) covalent geometry : angle 0.75655 (16951) hydrogen bonds : bond 0.05122 ( 473) hydrogen bonds : angle 4.85848 ( 1386) Misc. bond : bond 0.01183 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9297 (t0) cc_final: 0.9058 (t0) REVERT: B 163 ASP cc_start: 0.9025 (p0) cc_final: 0.8645 (p0) REVERT: B 207 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 293 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: B 415 GLU cc_start: 0.7617 (pp20) cc_final: 0.7238 (pp20) REVERT: B 417 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: B 422 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8253 (tp30) REVERT: B 425 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8872 (mmm) REVERT: K 185 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7836 (tm-30) REVERT: K 218 GLN cc_start: 0.9155 (mm110) cc_final: 0.8819 (mm-40) REVERT: K 334 GLU cc_start: 0.7615 (tm-30) cc_final: 0.6884 (tm-30) REVERT: L 12 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6036 (mmm) REVERT: L 71 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8712 (mmmm) REVERT: L 156 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.7956 (t-90) REVERT: L 214 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7332 (pp30) REVERT: L 289 SER cc_start: 0.8713 (m) cc_final: 0.8494 (p) REVERT: L 330 CYS cc_start: 0.9359 (t) cc_final: 0.9064 (p) REVERT: A 50 ASN cc_start: 0.8865 (t0) cc_final: 0.7833 (t0) REVERT: A 71 GLU cc_start: 0.7879 (tt0) cc_final: 0.7325 (tt0) REVERT: A 80 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9330 (p) REVERT: A 90 GLU cc_start: 0.8758 (tp30) cc_final: 0.8287 (tp30) REVERT: A 128 GLN cc_start: 0.8790 (tp40) cc_final: 0.8458 (tp-100) REVERT: A 154 MET cc_start: 0.9574 (mmp) cc_final: 0.9205 (mmm) REVERT: A 205 ASP cc_start: 0.9026 (p0) cc_final: 0.8774 (p0) REVERT: A 286 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9064 (mm) REVERT: A 290 GLU cc_start: 0.8787 (tt0) cc_final: 0.8399 (pt0) REVERT: A 302 MET cc_start: 0.9128 (mtt) cc_final: 0.8868 (mtt) REVERT: A 417 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8584 (mt-10) REVERT: A 423 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8771 (mm-30) outliers start: 62 outliers final: 27 residues processed: 236 average time/residue: 0.6004 time to fit residues: 153.5673 Evaluate side-chains 195 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 81 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.094368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065533 restraints weight = 28539.971| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.47 r_work: 0.2794 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12508 Z= 0.140 Angle : 0.612 7.890 16951 Z= 0.304 Chirality : 0.044 0.323 1874 Planarity : 0.004 0.042 2179 Dihedral : 11.731 179.587 1857 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.33 % Allowed : 19.51 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1515 helix: 1.61 (0.21), residues: 610 sheet: 0.09 (0.35), residues: 237 loop : -0.65 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 322 TYR 0.012 0.001 TYR K 274 PHE 0.016 0.001 PHE L 82 TRP 0.014 0.002 TRP A 388 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00319 (12507) covalent geometry : angle 0.61163 (16951) hydrogen bonds : bond 0.03971 ( 473) hydrogen bonds : angle 4.49939 ( 1386) Misc. bond : bond 0.00211 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9248 (t0) cc_final: 0.8953 (t0) REVERT: B 113 GLU cc_start: 0.9161 (mp0) cc_final: 0.8914 (mp0) REVERT: B 163 ASP cc_start: 0.9057 (p0) cc_final: 0.8668 (p0) REVERT: B 207 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8612 (tm-30) REVERT: B 293 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: B 301 MET cc_start: 0.9075 (tpp) cc_final: 0.8824 (mpp) REVERT: B 415 GLU cc_start: 0.7694 (pp20) cc_final: 0.7353 (pp20) REVERT: B 417 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: B 422 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8154 (tp30) REVERT: B 425 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8885 (mmm) REVERT: K 185 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7822 (tm-30) REVERT: K 218 GLN cc_start: 0.9226 (mm110) cc_final: 0.8829 (mm-40) REVERT: K 334 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7220 (tm-30) REVERT: L 12 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6064 (mmm) REVERT: L 33 PHE cc_start: 0.4308 (OUTLIER) cc_final: 0.3664 (t80) REVERT: L 71 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8814 (mmmm) REVERT: L 122 MET cc_start: 0.8959 (ptp) cc_final: 0.8240 (ptp) REVERT: L 156 HIS cc_start: 0.8991 (OUTLIER) cc_final: 0.8698 (t70) REVERT: L 214 GLN cc_start: 0.7909 (tm-30) cc_final: 0.6832 (pp30) REVERT: L 330 CYS cc_start: 0.9378 (t) cc_final: 0.9104 (p) REVERT: A 1 MET cc_start: 0.6963 (pmt) cc_final: 0.5977 (pmt) REVERT: A 48 SER cc_start: 0.8360 (m) cc_final: 0.8015 (p) REVERT: A 50 ASN cc_start: 0.8852 (t0) cc_final: 0.8113 (t0) REVERT: A 71 GLU cc_start: 0.7936 (tt0) cc_final: 0.7417 (tt0) REVERT: A 80 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9217 (p) REVERT: A 90 GLU cc_start: 0.8775 (tp30) cc_final: 0.8185 (tm-30) REVERT: A 128 GLN cc_start: 0.8936 (tp40) cc_final: 0.8472 (tp-100) REVERT: A 133 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: A 168 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 172 TYR cc_start: 0.9009 (t80) cc_final: 0.8773 (t80) REVERT: A 205 ASP cc_start: 0.8923 (p0) cc_final: 0.8640 (p0) REVERT: A 417 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8406 (mt-10) REVERT: A 423 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8779 (mm-30) REVERT: A 424 ASP cc_start: 0.9099 (m-30) cc_final: 0.8604 (t0) outliers start: 58 outliers final: 24 residues processed: 230 average time/residue: 0.5930 time to fit residues: 148.3190 Evaluate side-chains 190 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 33 PHE Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 434 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 125 optimal weight: 0.0770 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068867 restraints weight = 28206.523| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.32 r_work: 0.2869 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12508 Z= 0.122 Angle : 0.594 8.892 16951 Z= 0.294 Chirality : 0.044 0.272 1874 Planarity : 0.004 0.039 2179 Dihedral : 11.344 179.249 1857 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.56 % Allowed : 19.88 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1515 helix: 1.68 (0.21), residues: 611 sheet: 0.09 (0.35), residues: 237 loop : -0.59 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 322 TYR 0.010 0.001 TYR K 274 PHE 0.016 0.001 PHE L 82 TRP 0.019 0.002 TRP A 388 HIS 0.002 0.000 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00281 (12507) covalent geometry : angle 0.59446 (16951) hydrogen bonds : bond 0.03560 ( 473) hydrogen bonds : angle 4.35773 ( 1386) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9128 (t0) cc_final: 0.8884 (t0) REVERT: B 113 GLU cc_start: 0.9172 (mp0) cc_final: 0.8814 (mp0) REVERT: B 163 ASP cc_start: 0.8972 (p0) cc_final: 0.8320 (p0) REVERT: B 164 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8203 (mmp-170) REVERT: B 201 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9063 (p) REVERT: B 207 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 293 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8636 (tm-30) REVERT: B 338 LYS cc_start: 0.9219 (mmtm) cc_final: 0.8990 (mmtm) REVERT: B 358 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.7842 (pp) REVERT: B 373 MET cc_start: 0.9165 (mtm) cc_final: 0.8901 (mtm) REVERT: B 415 GLU cc_start: 0.7623 (pp20) cc_final: 0.7274 (pp20) REVERT: B 416 MET cc_start: 0.8522 (tpp) cc_final: 0.8293 (tpp) REVERT: B 417 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: B 422 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8253 (tp30) REVERT: B 425 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9007 (mmm) REVERT: K 218 GLN cc_start: 0.9234 (mm110) cc_final: 0.8829 (mm-40) REVERT: K 334 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7501 (tm-30) REVERT: L 51 VAL cc_start: 0.7580 (t) cc_final: 0.7375 (m) REVERT: L 71 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8759 (mmmm) REVERT: L 105 MET cc_start: 0.8236 (mmp) cc_final: 0.6457 (mtt) REVERT: L 134 TYR cc_start: 0.7991 (t80) cc_final: 0.7690 (t80) REVERT: L 170 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8619 (mm-30) REVERT: L 214 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7753 (pp30) REVERT: A 1 MET cc_start: 0.7084 (pmt) cc_final: 0.6035 (pmt) REVERT: A 48 SER cc_start: 0.8282 (m) cc_final: 0.7940 (p) REVERT: A 50 ASN cc_start: 0.8926 (t0) cc_final: 0.8210 (t0) REVERT: A 71 GLU cc_start: 0.7987 (tt0) cc_final: 0.7504 (tt0) REVERT: A 76 ASP cc_start: 0.9235 (m-30) cc_final: 0.8819 (m-30) REVERT: A 80 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9145 (p) REVERT: A 90 GLU cc_start: 0.8751 (tp30) cc_final: 0.8201 (tm-30) REVERT: A 98 ASP cc_start: 0.9083 (p0) cc_final: 0.8861 (p0) REVERT: A 128 GLN cc_start: 0.8971 (tp40) cc_final: 0.8443 (tp-100) REVERT: A 154 MET cc_start: 0.9514 (mmp) cc_final: 0.9150 (mmm) REVERT: A 168 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 205 ASP cc_start: 0.8955 (p0) cc_final: 0.8680 (p0) REVERT: A 402 ARG cc_start: 0.9502 (OUTLIER) cc_final: 0.9092 (ttm110) REVERT: A 423 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8675 (mm-30) REVERT: A 424 ASP cc_start: 0.9111 (m-30) cc_final: 0.8620 (t0) REVERT: A 430 LYS cc_start: 0.9295 (mppt) cc_final: 0.8917 (mppt) outliers start: 61 outliers final: 24 residues processed: 241 average time/residue: 0.6139 time to fit residues: 160.5326 Evaluate side-chains 199 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 HIS ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.093221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.064740 restraints weight = 28938.340| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.28 r_work: 0.2787 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12508 Z= 0.284 Angle : 0.685 8.710 16951 Z= 0.344 Chirality : 0.047 0.250 1874 Planarity : 0.004 0.035 2179 Dihedral : 11.375 177.224 1857 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.71 % Allowed : 20.25 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1515 helix: 1.53 (0.21), residues: 614 sheet: -0.08 (0.35), residues: 235 loop : -0.66 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.021 0.002 TYR K 274 PHE 0.021 0.002 PHE L 318 TRP 0.021 0.003 TRP A 346 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00646 (12507) covalent geometry : angle 0.68505 (16951) hydrogen bonds : bond 0.04436 ( 473) hydrogen bonds : angle 4.61354 ( 1386) Misc. bond : bond 0.00233 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9214 (t0) cc_final: 0.8929 (t0) REVERT: B 113 GLU cc_start: 0.9242 (mp0) cc_final: 0.8829 (mp0) REVERT: B 163 ASP cc_start: 0.8984 (p0) cc_final: 0.8354 (p0) REVERT: B 164 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8274 (mmp-170) REVERT: B 201 THR cc_start: 0.9576 (OUTLIER) cc_final: 0.9315 (p) REVERT: B 207 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 293 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8662 (tm-30) REVERT: B 308 ARG cc_start: 0.8658 (mpt-90) cc_final: 0.8425 (mpt-90) REVERT: B 358 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.7966 (pp) REVERT: B 373 MET cc_start: 0.9231 (mtm) cc_final: 0.8930 (mtm) REVERT: B 415 GLU cc_start: 0.7787 (pp20) cc_final: 0.7331 (pp20) REVERT: B 416 MET cc_start: 0.8653 (tpp) cc_final: 0.8343 (tpp) REVERT: B 417 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: B 422 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 425 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (tpp) REVERT: K 114 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8588 (t70) REVERT: K 218 GLN cc_start: 0.9229 (mm110) cc_final: 0.8808 (mm-40) REVERT: K 334 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7812 (tm-30) REVERT: L 12 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6502 (mmm) REVERT: L 71 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8749 (mmmm) REVERT: L 134 TYR cc_start: 0.8172 (t80) cc_final: 0.7903 (t80) REVERT: L 170 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8673 (mm-30) REVERT: L 221 GLN cc_start: 0.9220 (pm20) cc_final: 0.8897 (pm20) REVERT: L 270 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: L 282 MET cc_start: 0.8946 (tpp) cc_final: 0.8691 (tpp) REVERT: A 1 MET cc_start: 0.7187 (pmt) cc_final: 0.6212 (pmt) REVERT: A 48 SER cc_start: 0.8383 (m) cc_final: 0.8080 (p) REVERT: A 50 ASN cc_start: 0.8826 (t0) cc_final: 0.8120 (t0) REVERT: A 71 GLU cc_start: 0.7996 (tt0) cc_final: 0.7591 (tt0) REVERT: A 128 GLN cc_start: 0.9128 (tp40) cc_final: 0.8607 (tp-100) REVERT: A 172 TYR cc_start: 0.8982 (t80) cc_final: 0.8734 (t80) REVERT: A 205 ASP cc_start: 0.9017 (p0) cc_final: 0.8714 (p0) REVERT: A 402 ARG cc_start: 0.9545 (OUTLIER) cc_final: 0.9080 (mmt-90) REVERT: A 423 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8715 (mm-30) REVERT: A 424 ASP cc_start: 0.9158 (m-30) cc_final: 0.8688 (t0) outliers start: 63 outliers final: 29 residues processed: 208 average time/residue: 0.6100 time to fit residues: 137.4258 Evaluate side-chains 190 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 434 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 142 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067188 restraints weight = 29102.769| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.36 r_work: 0.2865 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12508 Z= 0.134 Angle : 0.611 9.409 16951 Z= 0.305 Chirality : 0.044 0.272 1874 Planarity : 0.004 0.036 2179 Dihedral : 11.121 178.237 1857 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.04 % Allowed : 21.45 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1515 helix: 1.57 (0.21), residues: 616 sheet: -0.12 (0.35), residues: 235 loop : -0.60 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 322 TYR 0.014 0.001 TYR L 84 PHE 0.016 0.001 PHE L 82 TRP 0.024 0.002 TRP A 388 HIS 0.002 0.000 HIS L 205 Details of bonding type rmsd covalent geometry : bond 0.00308 (12507) covalent geometry : angle 0.61147 (16951) hydrogen bonds : bond 0.03645 ( 473) hydrogen bonds : angle 4.42878 ( 1386) Misc. bond : bond 0.00112 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9135 (t0) cc_final: 0.8847 (t0) REVERT: B 113 GLU cc_start: 0.9156 (mp0) cc_final: 0.8789 (mp0) REVERT: B 163 ASP cc_start: 0.8970 (p0) cc_final: 0.8320 (p0) REVERT: B 164 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8221 (mmp-170) REVERT: B 201 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9241 (p) REVERT: B 293 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8643 (tm-30) REVERT: B 308 ARG cc_start: 0.8754 (mpt-90) cc_final: 0.8488 (mpt-90) REVERT: B 338 LYS cc_start: 0.9236 (mmtm) cc_final: 0.8758 (mmtm) REVERT: B 373 MET cc_start: 0.9064 (mtm) cc_final: 0.8826 (mtm) REVERT: B 398 MET cc_start: 0.8830 (mtp) cc_final: 0.8372 (ttm) REVERT: B 415 GLU cc_start: 0.7675 (pp20) cc_final: 0.7279 (pp20) REVERT: B 416 MET cc_start: 0.8596 (tpp) cc_final: 0.8313 (tpp) REVERT: B 417 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 422 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 425 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.8986 (tpp) REVERT: K 114 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8555 (t70) REVERT: K 218 GLN cc_start: 0.9215 (mm110) cc_final: 0.8774 (mm-40) REVERT: K 334 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7517 (tm-30) REVERT: K 341 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8751 (mtpm) REVERT: L 71 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8753 (mmmm) REVERT: L 105 MET cc_start: 0.7903 (mmp) cc_final: 0.6409 (mtt) REVERT: L 134 TYR cc_start: 0.8230 (t80) cc_final: 0.7960 (t80) REVERT: L 221 GLN cc_start: 0.9164 (pm20) cc_final: 0.8922 (pm20) REVERT: L 270 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: A 1 MET cc_start: 0.7122 (pmt) cc_final: 0.6201 (pmt) REVERT: A 50 ASN cc_start: 0.8903 (t0) cc_final: 0.8182 (t0) REVERT: A 71 GLU cc_start: 0.7991 (tt0) cc_final: 0.7619 (tt0) REVERT: A 76 ASP cc_start: 0.9237 (m-30) cc_final: 0.8842 (m-30) REVERT: A 128 GLN cc_start: 0.9084 (tp40) cc_final: 0.8637 (tp-100) REVERT: A 154 MET cc_start: 0.9477 (mmp) cc_final: 0.9103 (mmm) REVERT: A 168 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 205 ASP cc_start: 0.8988 (p0) cc_final: 0.8690 (p0) REVERT: A 313 MET cc_start: 0.9443 (mtm) cc_final: 0.9186 (mtt) REVERT: A 402 ARG cc_start: 0.9524 (OUTLIER) cc_final: 0.9132 (mmt-90) REVERT: A 423 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8651 (mm-30) REVERT: A 424 ASP cc_start: 0.9169 (m-30) cc_final: 0.8663 (t0) REVERT: A 430 LYS cc_start: 0.9300 (mppt) cc_final: 0.8946 (mppt) outliers start: 54 outliers final: 27 residues processed: 208 average time/residue: 0.6388 time to fit residues: 143.3319 Evaluate side-chains 185 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 135 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066339 restraints weight = 29038.672| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.29 r_work: 0.2822 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12508 Z= 0.176 Angle : 0.641 10.038 16951 Z= 0.320 Chirality : 0.044 0.237 1874 Planarity : 0.004 0.035 2179 Dihedral : 11.027 177.313 1857 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.19 % Allowed : 21.30 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1515 helix: 1.62 (0.21), residues: 610 sheet: -0.24 (0.35), residues: 242 loop : -0.60 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 322 TYR 0.014 0.001 TYR K 274 PHE 0.017 0.001 PHE L 82 TRP 0.038 0.003 TRP L 340 HIS 0.002 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00407 (12507) covalent geometry : angle 0.64078 (16951) hydrogen bonds : bond 0.03818 ( 473) hydrogen bonds : angle 4.40173 ( 1386) Misc. bond : bond 0.00153 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9174 (t0) cc_final: 0.8882 (t0) REVERT: B 71 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 113 GLU cc_start: 0.9211 (mp0) cc_final: 0.8800 (mp0) REVERT: B 163 ASP cc_start: 0.8970 (p0) cc_final: 0.8330 (p0) REVERT: B 164 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8216 (mmp-170) REVERT: B 201 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9204 (p) REVERT: B 293 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8662 (tm-30) REVERT: B 308 ARG cc_start: 0.8772 (mpt-90) cc_final: 0.8569 (mpt-90) REVERT: B 338 LYS cc_start: 0.9233 (mmtm) cc_final: 0.8734 (mmtm) REVERT: B 373 MET cc_start: 0.9073 (mtm) cc_final: 0.8867 (mtm) REVERT: B 398 MET cc_start: 0.8842 (mtp) cc_final: 0.8317 (ttm) REVERT: B 415 GLU cc_start: 0.7704 (pp20) cc_final: 0.7283 (pp20) REVERT: B 416 MET cc_start: 0.8572 (tpp) cc_final: 0.8288 (tpp) REVERT: B 422 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 425 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9003 (tpp) REVERT: K 114 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8581 (t70) REVERT: K 170 GLU cc_start: 0.8707 (mp0) cc_final: 0.8489 (mp0) REVERT: K 218 GLN cc_start: 0.9219 (mm110) cc_final: 0.8801 (mm-40) REVERT: K 336 THR cc_start: 0.5701 (OUTLIER) cc_final: 0.5398 (t) REVERT: L 12 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6561 (mmm) REVERT: L 71 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8786 (mmmm) REVERT: L 105 MET cc_start: 0.7759 (mmp) cc_final: 0.6508 (mtt) REVERT: L 122 MET cc_start: 0.8715 (ptp) cc_final: 0.7977 (ptp) REVERT: L 134 TYR cc_start: 0.8248 (t80) cc_final: 0.7970 (t80) REVERT: L 270 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: A 1 MET cc_start: 0.7163 (pmt) cc_final: 0.6167 (pmt) REVERT: A 50 ASN cc_start: 0.8890 (t0) cc_final: 0.8163 (t0) REVERT: A 71 GLU cc_start: 0.7953 (tt0) cc_final: 0.7603 (tt0) REVERT: A 76 ASP cc_start: 0.9252 (m-30) cc_final: 0.8873 (m-30) REVERT: A 80 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9158 (p) REVERT: A 128 GLN cc_start: 0.9127 (tp40) cc_final: 0.8688 (tp-100) REVERT: A 154 MET cc_start: 0.9538 (mmp) cc_final: 0.9126 (mmm) REVERT: A 205 ASP cc_start: 0.8997 (p0) cc_final: 0.8698 (p0) REVERT: A 313 MET cc_start: 0.9454 (mtm) cc_final: 0.9217 (mtt) REVERT: A 402 ARG cc_start: 0.9546 (OUTLIER) cc_final: 0.9166 (mmt-90) REVERT: A 423 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8703 (mm-30) REVERT: A 424 ASP cc_start: 0.9124 (m-30) cc_final: 0.8659 (t0) outliers start: 56 outliers final: 29 residues processed: 198 average time/residue: 0.6590 time to fit residues: 140.8947 Evaluate side-chains 183 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066611 restraints weight = 28347.018| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.25 r_work: 0.2831 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12508 Z= 0.163 Angle : 0.641 11.580 16951 Z= 0.320 Chirality : 0.044 0.240 1874 Planarity : 0.004 0.035 2179 Dihedral : 10.961 177.483 1857 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.66 % Allowed : 22.20 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1515 helix: 1.55 (0.21), residues: 610 sheet: -0.21 (0.35), residues: 240 loop : -0.60 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 322 TYR 0.013 0.001 TYR K 274 PHE 0.033 0.001 PHE L 318 TRP 0.060 0.004 TRP L 340 HIS 0.003 0.001 HIS L 205 Details of bonding type rmsd covalent geometry : bond 0.00381 (12507) covalent geometry : angle 0.64129 (16951) hydrogen bonds : bond 0.03732 ( 473) hydrogen bonds : angle 4.41752 ( 1386) Misc. bond : bond 0.00145 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9146 (t0) cc_final: 0.8839 (t0) REVERT: B 113 GLU cc_start: 0.9238 (mp0) cc_final: 0.8830 (mp0) REVERT: B 163 ASP cc_start: 0.8952 (p0) cc_final: 0.8313 (p0) REVERT: B 164 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8208 (mmp-170) REVERT: B 201 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9201 (p) REVERT: B 207 GLU cc_start: 0.8737 (tp30) cc_final: 0.8388 (tm-30) REVERT: B 293 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: B 308 ARG cc_start: 0.8811 (mpt-90) cc_final: 0.8610 (mpt-90) REVERT: B 338 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8929 (mmtm) REVERT: B 373 MET cc_start: 0.8926 (mtm) cc_final: 0.8720 (mtm) REVERT: B 398 MET cc_start: 0.8832 (mtp) cc_final: 0.8317 (ttm) REVERT: B 415 GLU cc_start: 0.7695 (pp20) cc_final: 0.7270 (pp20) REVERT: B 416 MET cc_start: 0.8562 (tpp) cc_final: 0.8308 (tpp) REVERT: B 422 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 425 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9000 (tpp) REVERT: K 114 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8577 (t70) REVERT: K 170 GLU cc_start: 0.8702 (mp0) cc_final: 0.8466 (mp0) REVERT: K 218 GLN cc_start: 0.9258 (mm110) cc_final: 0.8827 (mm-40) REVERT: L 71 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8728 (mmmm) REVERT: L 105 MET cc_start: 0.7856 (mmp) cc_final: 0.6582 (mtt) REVERT: L 134 TYR cc_start: 0.8239 (t80) cc_final: 0.7984 (t80) REVERT: L 270 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: L 282 MET cc_start: 0.8985 (tpp) cc_final: 0.8729 (tpp) REVERT: A 1 MET cc_start: 0.7167 (pmt) cc_final: 0.6505 (pmt) REVERT: A 50 ASN cc_start: 0.8942 (t0) cc_final: 0.8283 (t160) REVERT: A 71 GLU cc_start: 0.7978 (tt0) cc_final: 0.7606 (tt0) REVERT: A 76 ASP cc_start: 0.9247 (m-30) cc_final: 0.8864 (m-30) REVERT: A 80 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9128 (p) REVERT: A 128 GLN cc_start: 0.9131 (tp40) cc_final: 0.8688 (tp-100) REVERT: A 133 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: A 154 MET cc_start: 0.9516 (mmp) cc_final: 0.9144 (mmm) REVERT: A 205 ASP cc_start: 0.9005 (p0) cc_final: 0.8702 (p0) REVERT: A 313 MET cc_start: 0.9455 (mtm) cc_final: 0.9179 (mtt) REVERT: A 402 ARG cc_start: 0.9550 (OUTLIER) cc_final: 0.9177 (mmt-90) REVERT: A 423 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8691 (mm-30) REVERT: A 424 ASP cc_start: 0.9129 (m-30) cc_final: 0.8665 (t0) REVERT: A 430 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8903 (mppt) outliers start: 49 outliers final: 29 residues processed: 196 average time/residue: 0.6511 time to fit residues: 138.1133 Evaluate side-chains 185 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064573 restraints weight = 27941.913| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.17 r_work: 0.2818 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12508 Z= 0.245 Angle : 0.686 11.620 16951 Z= 0.343 Chirality : 0.045 0.250 1874 Planarity : 0.004 0.035 2179 Dihedral : 11.018 176.247 1857 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.36 % Allowed : 22.50 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.22), residues: 1515 helix: 1.52 (0.21), residues: 609 sheet: -0.27 (0.35), residues: 235 loop : -0.61 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 322 TYR 0.018 0.001 TYR K 274 PHE 0.017 0.001 PHE L 82 TRP 0.047 0.004 TRP L 340 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00561 (12507) covalent geometry : angle 0.68601 (16951) hydrogen bonds : bond 0.04235 ( 473) hydrogen bonds : angle 4.56893 ( 1386) Misc. bond : bond 0.00213 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9190 (t0) cc_final: 0.8880 (t0) REVERT: B 113 GLU cc_start: 0.9207 (mp0) cc_final: 0.8780 (mp0) REVERT: B 164 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8344 (mmp-170) REVERT: B 201 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9279 (p) REVERT: B 207 GLU cc_start: 0.8771 (tp30) cc_final: 0.8404 (tm-30) REVERT: B 293 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: B 308 ARG cc_start: 0.8778 (mpt-90) cc_final: 0.8531 (mpt-90) REVERT: B 373 MET cc_start: 0.9019 (mtm) cc_final: 0.8770 (mtm) REVERT: B 415 GLU cc_start: 0.7762 (pp20) cc_final: 0.7312 (pp20) REVERT: B 416 MET cc_start: 0.8616 (tpp) cc_final: 0.8287 (tpp) REVERT: B 422 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 425 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8962 (tpp) REVERT: K 114 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8653 (t70) REVERT: K 218 GLN cc_start: 0.9259 (mm110) cc_final: 0.8815 (mm-40) REVERT: L 105 MET cc_start: 0.7959 (mmp) cc_final: 0.6676 (mtt) REVERT: L 170 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8642 (mm-30) REVERT: L 270 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: A 1 MET cc_start: 0.7225 (pmt) cc_final: 0.6408 (pmt) REVERT: A 50 ASN cc_start: 0.8842 (t0) cc_final: 0.8173 (t160) REVERT: A 71 GLU cc_start: 0.7927 (tt0) cc_final: 0.7560 (tt0) REVERT: A 76 ASP cc_start: 0.9251 (m-30) cc_final: 0.8868 (m-30) REVERT: A 80 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9178 (p) REVERT: A 113 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8611 (mp0) REVERT: A 128 GLN cc_start: 0.9186 (tp40) cc_final: 0.8735 (tp-100) REVERT: A 154 MET cc_start: 0.9517 (mmp) cc_final: 0.9139 (mmm) REVERT: A 205 ASP cc_start: 0.9039 (p0) cc_final: 0.8747 (p0) REVERT: A 313 MET cc_start: 0.9450 (mtm) cc_final: 0.9186 (mtt) REVERT: A 402 ARG cc_start: 0.9559 (OUTLIER) cc_final: 0.9127 (mmt-90) REVERT: A 423 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8691 (mm-30) REVERT: A 424 ASP cc_start: 0.9164 (m-30) cc_final: 0.8685 (t0) outliers start: 45 outliers final: 26 residues processed: 183 average time/residue: 0.6552 time to fit residues: 129.7168 Evaluate side-chains 177 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 402 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066951 restraints weight = 28130.591| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.27 r_work: 0.2846 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12508 Z= 0.134 Angle : 0.654 13.376 16951 Z= 0.323 Chirality : 0.044 0.245 1874 Planarity : 0.004 0.037 2179 Dihedral : 10.903 177.649 1857 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.69 % Allowed : 22.94 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.22), residues: 1515 helix: 1.54 (0.21), residues: 609 sheet: -0.20 (0.35), residues: 233 loop : -0.62 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 322 TYR 0.012 0.001 TYR L 84 PHE 0.037 0.001 PHE L 318 TRP 0.047 0.003 TRP A 388 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00314 (12507) covalent geometry : angle 0.65435 (16951) hydrogen bonds : bond 0.03597 ( 473) hydrogen bonds : angle 4.40280 ( 1386) Misc. bond : bond 0.00121 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9128 (t0) cc_final: 0.8819 (t0) REVERT: B 113 GLU cc_start: 0.9211 (mp0) cc_final: 0.8808 (mp0) REVERT: B 164 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8277 (mmp-170) REVERT: B 201 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9199 (p) REVERT: B 207 GLU cc_start: 0.8755 (tp30) cc_final: 0.8453 (tm-30) REVERT: B 293 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8639 (tm-30) REVERT: B 308 ARG cc_start: 0.8812 (mpt-90) cc_final: 0.8589 (mpt-90) REVERT: B 398 MET cc_start: 0.8775 (mtp) cc_final: 0.8372 (ttm) REVERT: B 415 GLU cc_start: 0.7717 (pp20) cc_final: 0.7341 (pp20) REVERT: B 416 MET cc_start: 0.8540 (tpp) cc_final: 0.8309 (tpp) REVERT: B 422 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 425 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8983 (tpp) REVERT: K 114 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8623 (t70) REVERT: K 218 GLN cc_start: 0.9258 (mm110) cc_final: 0.8811 (mm-40) REVERT: L 71 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8715 (mmmm) REVERT: L 105 MET cc_start: 0.7872 (mmp) cc_final: 0.6618 (mtt) REVERT: L 156 HIS cc_start: 0.8855 (t70) cc_final: 0.8375 (t-90) REVERT: L 203 ARG cc_start: 0.1322 (tpt170) cc_final: 0.0910 (tpt90) REVERT: L 270 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: L 330 CYS cc_start: 0.9168 (t) cc_final: 0.8936 (p) REVERT: L 340 TRP cc_start: 0.8692 (m100) cc_final: 0.8046 (m-90) REVERT: A 1 MET cc_start: 0.7113 (pmt) cc_final: 0.6345 (pmt) REVERT: A 50 ASN cc_start: 0.8884 (t0) cc_final: 0.8220 (t160) REVERT: A 71 GLU cc_start: 0.7974 (tt0) cc_final: 0.7574 (tt0) REVERT: A 76 ASP cc_start: 0.9245 (m-30) cc_final: 0.8836 (m-30) REVERT: A 80 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9102 (p) REVERT: A 128 GLN cc_start: 0.9175 (tp40) cc_final: 0.8720 (tp-100) REVERT: A 154 MET cc_start: 0.9532 (mmp) cc_final: 0.9172 (mmm) REVERT: A 205 ASP cc_start: 0.8992 (p0) cc_final: 0.8687 (p0) REVERT: A 313 MET cc_start: 0.9429 (mtm) cc_final: 0.9164 (mtt) REVERT: A 402 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.9173 (mmt-90) REVERT: A 423 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8675 (mm-30) REVERT: A 424 ASP cc_start: 0.9170 (m-30) cc_final: 0.8675 (t0) REVERT: A 430 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8897 (mppt) outliers start: 36 outliers final: 21 residues processed: 185 average time/residue: 0.6745 time to fit residues: 134.7681 Evaluate side-chains 176 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain K residue 7 CYS Chi-restraints excluded: chain K residue 12 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 270 GLU Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 136 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 ASN ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063712 restraints weight = 28290.298| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.23 r_work: 0.2774 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12508 Z= 0.283 Angle : 0.729 13.538 16951 Z= 0.362 Chirality : 0.047 0.251 1874 Planarity : 0.004 0.039 2179 Dihedral : 11.043 175.406 1857 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.69 % Allowed : 23.62 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1515 helix: 1.39 (0.21), residues: 615 sheet: -0.34 (0.35), residues: 234 loop : -0.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 322 TYR 0.019 0.001 TYR K 274 PHE 0.031 0.002 PHE L 318 TRP 0.069 0.005 TRP A 388 HIS 0.003 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00648 (12507) covalent geometry : angle 0.72924 (16951) hydrogen bonds : bond 0.04416 ( 473) hydrogen bonds : angle 4.62754 ( 1386) Misc. bond : bond 0.00231 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4574.13 seconds wall clock time: 78 minutes 50.11 seconds (4730.11 seconds total)