Starting phenix.real_space_refine on Mon Dec 30 04:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_19176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_19176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_19176.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_19176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhh_19176/12_2024/8rhh_19176.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.42, per 1000 atoms: 0.61 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.14 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: 3.53 Time building geometry restraints manager: 3.63 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.670 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.140 ------------------------------------------------------------------------------- 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 : 0.005 0.175 12507 Z= 0.329 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS A 283 PHE 0.016 0.001 PHE K 82 TYR 0.012 0.001 TYR K 29 ARG 0.003 0.000 ARG K 14 *********************** 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 : 1.458 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: B 163 ASP cc_start: 0.7797 (p0) cc_final: 0.7575 (p0) REVERT: K 9 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8520 (mt) 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: 0.8091 (mm) outliers start: 2 outliers final: 3 residues processed: 366 average time/residue: 1.4122 time to fit residues: 556.0134 Evaluate side-chains 188 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 125 optimal weight: 10.0000 chunk 112 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN B 206 ASN ** B 294 GLN ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12507 Z= 0.225 Angle : 0.674 12.712 16951 Z= 0.331 Chirality : 0.045 0.302 1874 Planarity : 0.004 0.046 2179 Dihedral : 14.882 173.539 1866 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.44 % Allowed : 18.61 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1515 helix: 1.57 (0.21), residues: 606 sheet: 0.21 (0.34), residues: 247 loop : -0.81 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.002 0.001 HIS B 229 PHE 0.022 0.001 PHE L 318 TYR 0.031 0.001 TYR L 274 ARG 0.008 0.001 ARG A 308 *********************** 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 252 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 1.499 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 163 ASP cc_start: 0.7938 (p0) cc_final: 0.7669 (p0) REVERT: B 201 THR cc_start: 0.9244 (t) cc_final: 0.8875 (p) REVERT: B 207 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 417 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: B 422 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7920 (tp30) REVERT: K 334 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 50 ASN cc_start: 0.8061 (t0) cc_final: 0.7622 (t0) REVERT: A 71 GLU cc_start: 0.7562 (tt0) cc_final: 0.7264 (tt0) REVERT: A 168 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 417 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7556 (mt-10) outliers start: 46 outliers final: 19 residues processed: 239 average time/residue: 1.2511 time to fit residues: 325.8702 Evaluate side-chains 184 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 417 GLU 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 L residue 11 VAL Chi-restraints excluded: chain L residue 86 GLN 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 188 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 295 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 0.0980 chunk 146 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 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 125 ASN ** L 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12507 Z= 0.426 Angle : 0.686 7.655 16951 Z= 0.345 Chirality : 0.047 0.343 1874 Planarity : 0.004 0.043 2179 Dihedral : 11.950 178.738 1857 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.01 % Allowed : 19.21 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1515 helix: 1.51 (0.21), residues: 610 sheet: 0.14 (0.35), residues: 224 loop : -0.76 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP L 340 HIS 0.003 0.001 HIS A 139 PHE 0.017 0.002 PHE L 82 TYR 0.016 0.002 TYR K 274 ARG 0.008 0.001 ARG A 264 *********************** 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 222 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 155 time to evaluate : 1.124 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 163 ASP cc_start: 0.8131 (p0) cc_final: 0.7836 (p0) REVERT: B 207 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 417 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: A 1 MET cc_start: 0.6655 (pmt) cc_final: 0.5906 (pmt) REVERT: A 71 GLU cc_start: 0.7851 (tt0) cc_final: 0.7473 (tt0) REVERT: A 172 TYR cc_start: 0.8403 (t80) cc_final: 0.8203 (t80) outliers start: 67 outliers final: 37 residues processed: 207 average time/residue: 1.2292 time to fit residues: 278.4045 Evaluate side-chains 181 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 166 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 12 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 151 THR Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 211 ASN 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 107 ILE 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 48 SER Chi-restraints excluded: chain A residue 51 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 295 CYS Chi-restraints excluded: chain A residue 344 VAL 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 133 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12507 Z= 0.188 Angle : 0.608 9.183 16951 Z= 0.303 Chirality : 0.043 0.282 1874 Planarity : 0.004 0.037 2179 Dihedral : 11.499 179.935 1857 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.41 % Allowed : 19.58 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1515 helix: 1.67 (0.21), residues: 610 sheet: 0.06 (0.35), residues: 235 loop : -0.66 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 388 HIS 0.002 0.000 HIS L 205 PHE 0.015 0.001 PHE L 82 TYR 0.010 0.001 TYR K 274 ARG 0.007 0.001 ARG B 322 *********************** 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 231 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 1.773 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 163 ASP cc_start: 0.7992 (p0) cc_final: 0.7546 (p0) REVERT: B 164 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7901 (mmp-170) REVERT: B 201 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9102 (p) REVERT: B 207 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 417 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: B 422 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8058 (tp30) REVERT: L 156 HIS cc_start: 0.6159 (t-90) cc_final: 0.5865 (t-90) REVERT: L 219 THR cc_start: 0.8227 (p) cc_final: 0.7826 (t) REVERT: L 221 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8302 (pm20) REVERT: A 71 GLU cc_start: 0.7746 (tt0) cc_final: 0.7495 (tt0) outliers start: 59 outliers final: 18 residues processed: 220 average time/residue: 1.2703 time to fit residues: 304.5403 Evaluate side-chains 173 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 374 SER Chi-restraints excluded: chain B residue 417 GLU 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 268 LEU Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 344 TYR Chi-restraints excluded: chain A residue 48 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 122 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12507 Z= 0.248 Angle : 0.606 8.610 16951 Z= 0.306 Chirality : 0.044 0.248 1874 Planarity : 0.004 0.034 2179 Dihedral : 11.363 178.879 1857 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.81 % Allowed : 21.00 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1515 helix: 1.59 (0.21), residues: 616 sheet: -0.06 (0.35), residues: 235 loop : -0.65 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 388 HIS 0.002 0.001 HIS L 205 PHE 0.016 0.001 PHE L 82 TYR 0.013 0.001 TYR K 274 ARG 0.006 0.000 ARG B 322 *********************** 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 208 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.483 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 163 ASP cc_start: 0.8038 (p0) cc_final: 0.7595 (p0) REVERT: B 164 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7941 (mmp-170) REVERT: B 201 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9126 (p) REVERT: B 358 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8220 (pp) REVERT: B 417 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: B 422 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8082 (tp30) REVERT: B 425 MET cc_start: 0.8805 (mmm) cc_final: 0.8563 (tpp) REVERT: L 221 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8008 (pm20) REVERT: L 282 MET cc_start: 0.7485 (tpp) cc_final: 0.7238 (tpp) REVERT: A 71 GLU cc_start: 0.7800 (tt0) cc_final: 0.7561 (tt0) REVERT: A 402 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8728 (mmt-90) outliers start: 51 outliers final: 25 residues processed: 202 average time/residue: 1.2682 time to fit residues: 278.6165 Evaluate side-chains 171 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 358 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU 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 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 221 GLN 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 48 SER Chi-restraints excluded: chain A residue 188 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12507 Z= 0.284 Angle : 0.631 9.208 16951 Z= 0.317 Chirality : 0.044 0.232 1874 Planarity : 0.004 0.032 2179 Dihedral : 11.229 178.031 1857 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.96 % Allowed : 21.60 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1515 helix: 1.65 (0.21), residues: 610 sheet: -0.19 (0.35), residues: 233 loop : -0.64 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 388 HIS 0.002 0.001 HIS A 139 PHE 0.016 0.001 PHE L 82 TYR 0.014 0.001 TYR K 274 ARG 0.006 0.000 ARG B 322 *********************** 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 204 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.520 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 163 ASP cc_start: 0.8043 (p0) cc_final: 0.7632 (p0) REVERT: B 164 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7956 (mmp-170) REVERT: B 201 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9133 (p) REVERT: B 358 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8384 (pp) REVERT: B 422 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8081 (tp30) REVERT: L 12 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6626 (mmm) REVERT: L 221 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: A 71 GLU cc_start: 0.7790 (tt0) cc_final: 0.7588 (tt0) REVERT: A 269 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9218 (pp) REVERT: A 402 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8741 (mmt-90) outliers start: 53 outliers final: 29 residues processed: 192 average time/residue: 1.2622 time to fit residues: 265.1243 Evaluate side-chains 178 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 114 LEU 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 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 374 SER 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 247 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 221 GLN 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 48 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 434 GLU 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 138 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12507 Z= 0.236 Angle : 0.630 10.191 16951 Z= 0.315 Chirality : 0.043 0.225 1874 Planarity : 0.004 0.033 2179 Dihedral : 11.115 178.073 1857 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.59 % Allowed : 22.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1515 helix: 1.62 (0.21), residues: 610 sheet: -0.21 (0.35), residues: 233 loop : -0.58 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 340 HIS 0.002 0.000 HIS A 8 PHE 0.017 0.001 PHE L 82 TYR 0.017 0.001 TYR K 274 ARG 0.007 0.000 ARG B 322 *********************** 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 195 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.534 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 201 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9122 (p) REVERT: B 417 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: L 12 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6693 (mmm) REVERT: L 221 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: A 269 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9204 (pp) outliers start: 48 outliers final: 31 residues processed: 185 average time/residue: 1.3054 time to fit residues: 262.4502 Evaluate side-chains 173 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 114 LEU 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 201 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 417 GLU 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 126 LEU 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 325 ILE Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 221 GLN 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 48 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 344 VAL 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 88 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 93 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 12507 Z= 0.483 Angle : 0.741 10.727 16951 Z= 0.373 Chirality : 0.047 0.229 1874 Planarity : 0.004 0.032 2179 Dihedral : 11.265 175.446 1857 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 4.04 % Allowed : 22.20 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1515 helix: 1.33 (0.21), residues: 613 sheet: -0.26 (0.36), residues: 220 loop : -0.77 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 388 HIS 0.003 0.001 HIS A 283 PHE 0.019 0.002 PHE A 395 TYR 0.022 0.002 TYR K 274 ARG 0.007 0.001 ARG B 322 *********************** 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 190 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 136 time to evaluate : 1.449 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: B 425 MET cc_start: 0.8849 (mmm) cc_final: 0.8597 (tpp) REVERT: L 12 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6922 (mmm) REVERT: L 221 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: A 269 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9277 (pp) REVERT: A 413 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8390 (ttp) outliers start: 54 outliers final: 27 residues processed: 176 average time/residue: 1.2387 time to fit residues: 237.6799 Evaluate side-chains 157 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 SER 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 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 203 ARG Chi-restraints excluded: chain L residue 221 GLN 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 48 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12507 Z= 0.224 Angle : 0.667 11.372 16951 Z= 0.332 Chirality : 0.045 0.361 1874 Planarity : 0.004 0.035 2179 Dihedral : 11.091 177.533 1857 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 23.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1515 helix: 1.47 (0.21), residues: 614 sheet: -0.38 (0.35), residues: 229 loop : -0.65 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 388 HIS 0.002 0.001 HIS K 200 PHE 0.016 0.001 PHE L 82 TYR 0.011 0.001 TYR K 274 ARG 0.008 0.001 ARG B 322 *********************** 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 182 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.480 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: B 425 MET cc_start: 0.8720 (mmm) cc_final: 0.8473 (tpp) REVERT: K 114 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (t70) REVERT: L 12 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: L 221 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: A 36 MET cc_start: 0.8186 (tmm) cc_final: 0.7959 (tmm) REVERT: A 154 MET cc_start: 0.8387 (mmm) cc_final: 0.7780 (mmm) REVERT: A 269 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9201 (pp) outliers start: 38 outliers final: 24 residues processed: 173 average time/residue: 1.3649 time to fit residues: 258.3899 Evaluate side-chains 160 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 129 CYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 SER 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 12 MET Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 203 ARG Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 261 LEU 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 188 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12507 Z= 0.216 Angle : 0.682 10.905 16951 Z= 0.337 Chirality : 0.044 0.345 1874 Planarity : 0.004 0.038 2179 Dihedral : 10.992 177.007 1857 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.39 % Allowed : 24.29 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1515 helix: 1.48 (0.21), residues: 612 sheet: -0.33 (0.35), residues: 233 loop : -0.62 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP L 340 HIS 0.002 0.001 HIS A 8 PHE 0.038 0.001 PHE L 318 TYR 0.020 0.001 TYR L 118 ARG 0.009 0.001 ARG B 322 ********************** 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 176 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.455 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: K 114 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8282 (t70) REVERT: A 377 MET cc_start: 0.8421 (tmm) cc_final: 0.8148 (tmm) REVERT: A 398 MET cc_start: 0.8189 (mtp) cc_final: 0.7919 (ttm) outliers start: 32 outliers final: 21 residues processed: 170 average time/residue: 1.2986 time to fit residues: 240.5412 Evaluate side-chains 158 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 220 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain K residue 39 VAL 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 261 LEU 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 188 ILE Chi-restraints excluded: chain A residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3511 r_free = 0.3511 target = 0.092800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064932 restraints weight = 28744.688| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.18 r_work: 0.2787 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 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: 0.8501 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12507 Z= 0.445 Angle : 0.775 12.313 16951 Z= 0.386 Chirality : 0.048 0.304 1874 Planarity : 0.004 0.038 2179 Dihedral : 11.172 175.173 1857 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 2.09 % Allowed : 24.96 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1515 helix: 1.26 (0.21), residues: 612 sheet: -0.32 (0.37), residues: 219 loop : -0.80 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP L 340 HIS 0.004 0.001 HIS B 139 PHE 0.032 0.002 PHE L 318 TYR 0.023 0.002 TYR K 274 ARG 0.009 0.001 ARG B 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4798.82 seconds wall clock time: 86 minutes 58.48 seconds (5218.48 seconds total)