Starting phenix.real_space_refine on Wed Sep 17 15:42:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhb_19174/09_2025/8rhb_19174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhb_19174/09_2025/8rhb_19174.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/8rhb_19174/09_2025/8rhb_19174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhb_19174/09_2025/8rhb_19174.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhb_19174/09_2025/8rhb_19174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhb_19174/09_2025/8rhb_19174.cif" } 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 8 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 5981 2.51 5 N 1625 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 9539 Number of models: 1 Model: "" Number of chains: 9 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: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2585 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 8, 'TRANS': 321} 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: 43 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 6, 43 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "t" Number of atoms: 47 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 2, 'TRANS': 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "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: "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: 12 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 BALA t 921 " occ=0.50 ... (3 atoms not shown) pdb=" CB BALA t 921 " occ=0.50 residue: pdb=" N BLYS t 922 " occ=0.50 ... (7 atoms not shown) pdb=" NZ BLYS t 922 " occ=0.50 residue: pdb=" N BPRO t 923 " occ=0.50 ... (5 atoms not shown) pdb=" CD BPRO t 923 " occ=0.50 residue: pdb=" N BILE t 936 " occ=0.50 ... (6 atoms not shown) pdb=" CD1BILE t 936 " occ=0.50 residue: pdb=" N BARG t 937 " occ=0.50 ... (9 atoms not shown) pdb=" NH2BARG t 937 " occ=0.50 residue: pdb=" N BPRO t 938 " occ=0.50 ... (5 atoms not shown) pdb=" CD BPRO t 938 " occ=0.50 Time building chain proxies: 2.42, per 1000 atoms: 0.25 Number of scatterers: 9539 At special positions: 0 Unit cell: (73.644, 106.134, 111.549, 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 64 16.00 P 8 15.00 Mg 2 11.99 O 1859 8.00 N 1625 7.00 C 5981 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: 1.00 Conformation dependent library (CDL) restraints added in 395.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 47.2% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.961A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.432A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.120A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.383A 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: 3.945A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.606A 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: 3.905A 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 287 through 296 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.552A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.263A 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: 3.531A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.630A 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 122 removed outlier: 3.575A pdb=" N ARG K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 189 removed outlier: 3.611A pdb=" N VAL K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 3.533A 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: 4.011A 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 324 removed outlier: 4.085A pdb=" N THR K 324 " --> pdb=" O GLN K 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.553A 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 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.545A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 5.160A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.142A 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 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.756A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.761A 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 278 through 282 removed outlier: 3.795A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.616A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.073A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.849A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.243A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.889A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 273 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 6 through 8 Processing sheet with id=AA3, first strand: chain 'K' and resid 10 through 15 removed outlier: 7.476A pdb=" N VAL K 11 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE K 52 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.676A 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 50 through 52 current: chain 'K' and resid 142 through 144 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 142 through 144 current: chain 'K' and resid 222 through 223 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.608A pdb=" N GLN K 34 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 154 through 157 removed outlier: 4.505A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.867A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N SER A 165 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.809A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1182 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: 1.62 Time building geometry restraints manager: 1.24 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: 1695 1.32 - 1.44: 2514 1.44 - 1.57: 5417 1.57 - 1.69: 16 1.69 - 1.81: 99 Bond restraints: 9741 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=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 1.795 1.668 0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" O5' ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 1.655 1.538 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O3A ANP K1001 " pdb=" PA ANP K1001 " ideal model delta sigma weight residual 1.613 1.515 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5' ANP K1001 " pdb=" O5' ANP K1001 " ideal model delta sigma weight residual 1.409 1.329 0.080 2.00e-02 2.50e+03 1.58e+01 ... (remaining 9736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 13183 4.35 - 8.69: 30 8.69 - 13.04: 6 13.04 - 17.38: 1 17.38 - 21.73: 1 Bond angle restraints: 13221 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 99.88 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" PB ANP K1001 " pdb=" N3B ANP K1001 " pdb=" PG ANP K1001 " ideal model delta sigma weight residual 126.95 114.44 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " pdb=" C20 TA1 B 502 " ideal model delta sigma weight residual 104.78 116.29 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" N VAL A 182 " pdb=" CA VAL A 182 " pdb=" C VAL A 182 " ideal model delta sigma weight residual 111.91 108.81 3.10 8.90e-01 1.26e+00 1.21e+01 ... (remaining 13216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 5756 34.05 - 68.09: 146 68.09 - 102.14: 6 102.14 - 136.19: 16 136.19 - 170.23: 6 Dihedral angle restraints: 5930 sinusoidal: 2466 harmonic: 3464 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 -120.50 -170.23 1 2.00e+01 2.50e-03 4.77e+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 -52.39 156.99 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 274.12 135.11 139.01 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 5927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1267 0.066 - 0.131: 182 0.131 - 0.197: 6 0.197 - 0.262: 1 0.262 - 0.328: 2 Chirality restraints: 1458 Sorted by residual: 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 2.69e+00 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 -2.77 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C2' ANP K1001 " pdb=" C1' ANP K1001 " pdb=" C3' ANP K1001 " pdb=" O2' ANP K1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.51 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1455 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ANP K1001 " 0.042 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 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ANP K1001 " 0.001 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 " 0.011 2.00e-02 2.50e+03 pdb=" N7 ANP K1001 " 0.002 2.00e-02 2.50e+03 pdb=" N9 ANP K1001 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 325 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 89 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.021 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 41 2.43 - 3.05: 6111 3.05 - 3.67: 14367 3.67 - 4.28: 21574 4.28 - 4.90: 36409 Nonbonded interactions: 78502 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.818 2.170 nonbonded pdb=" OG SER K 202 " pdb="MG MG K1002 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR K 92 " pdb="MG MG K1002 " model vdw 2.167 2.170 nonbonded pdb=" CD GLU A 71 " pdb="MG MG A 502 " model vdw 2.192 2.400 nonbonded pdb=" OG SER A 165 " pdb=" OE1 GLN A 256 " model vdw 2.209 3.040 ... (remaining 78497 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3126 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 : 0.010 0.879 9742 Z= 0.922 Angle : 0.669 21.728 13221 Z= 0.308 Chirality : 0.046 0.328 1458 Planarity : 0.003 0.039 1708 Dihedral : 17.120 170.233 3704 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.48 (0.24), residues: 1184 helix: 2.05 (0.24), residues: 468 sheet: -0.39 (0.38), residues: 202 loop : -1.02 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 25 TYR 0.011 0.001 TYR B 161 PHE 0.017 0.001 PHE K 82 TRP 0.010 0.001 TRP A 346 HIS 0.003 0.001 HIS K 129 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 9741) covalent geometry : angle 0.66936 (13221) hydrogen bonds : bond 0.15228 ( 402) hydrogen bonds : angle 5.71124 ( 1182) Misc. bond : bond 0.87898 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.382 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 393 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 358 GLN cc_start: 0.2757 (tp40) cc_final: 0.2556 (pt0) outliers start: 0 outliers final: 2 residues processed: 275 average time/residue: 0.5881 time to fit residues: 172.9716 Evaluate side-chains 145 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 244 GLU Chi-restraints excluded: chain A residue 127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS B 206 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN K 129 HIS K 211 ASN K 214 GLN K 327 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089915 restraints weight = 19086.707| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.41 r_work: 0.3189 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4234 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9742 Z= 0.155 Angle : 0.773 15.252 13221 Z= 0.371 Chirality : 0.047 0.296 1458 Planarity : 0.005 0.080 1708 Dihedral : 15.107 175.817 1465 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.65 % Allowed : 18.49 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.08 (0.24), residues: 1184 helix: 1.20 (0.23), residues: 493 sheet: -0.24 (0.37), residues: 201 loop : -0.96 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 243 TYR 0.018 0.002 TYR A 103 PHE 0.017 0.002 PHE A 244 TRP 0.047 0.003 TRP B 21 HIS 0.024 0.002 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9741) covalent geometry : angle 0.77251 (13221) hydrogen bonds : bond 0.04522 ( 402) hydrogen bonds : angle 4.94563 ( 1182) Misc. bond : bond 0.00463 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.305 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: B 1 MET cc_start: 0.2266 (mmp) cc_final: -0.0302 (pmm) REVERT: B 393 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 80 THR cc_start: 0.7035 (OUTLIER) cc_final: 0.6703 (p) outliers start: 48 outliers final: 10 residues processed: 191 average time/residue: 0.4739 time to fit residues: 98.5849 Evaluate side-chains 141 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS A 101 ASN A 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092801 restraints weight = 18825.324| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.45 r_work: 0.3238 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4486 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9742 Z= 0.137 Angle : 0.709 15.643 13221 Z= 0.342 Chirality : 0.045 0.372 1458 Planarity : 0.005 0.093 1708 Dihedral : 12.325 177.266 1460 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.19 % Allowed : 19.85 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.11 (0.24), residues: 1184 helix: 1.08 (0.23), residues: 486 sheet: -0.06 (0.39), residues: 201 loop : -0.82 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 278 TYR 0.020 0.002 TYR B 342 PHE 0.018 0.001 PHE B 20 TRP 0.022 0.002 TRP B 346 HIS 0.014 0.001 HIS B 28 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9741) covalent geometry : angle 0.70921 (13221) hydrogen bonds : bond 0.04085 ( 402) hydrogen bonds : angle 4.69465 ( 1182) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.296 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: B 1 MET cc_start: 0.2752 (mmp) cc_final: 0.0042 (pmm) REVERT: B 269 MET cc_start: 0.5298 (mmm) cc_final: 0.4692 (tmm) REVERT: B 393 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7124 (tm-30) REVERT: K 119 ILE cc_start: 0.3568 (tt) cc_final: 0.3165 (tt) REVERT: A 176 GLN cc_start: 0.7260 (mm110) cc_final: 0.6983 (mm110) outliers start: 33 outliers final: 14 residues processed: 167 average time/residue: 0.4612 time to fit residues: 84.1810 Evaluate side-chains 142 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 344 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS B 294 GLN B 309 HIS B 350 ASN K 117 ASN K 129 HIS ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 ASN K 214 GLN A 18 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106359 restraints weight = 19446.744| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.68 r_work: 0.3458 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 1.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 9742 Z= 0.349 Angle : 1.118 15.258 13221 Z= 0.590 Chirality : 0.061 0.310 1458 Planarity : 0.008 0.078 1708 Dihedral : 12.735 161.216 1460 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 6.68 % Allowed : 17.81 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -1.33 (0.23), residues: 1184 helix: -0.46 (0.21), residues: 464 sheet: -0.43 (0.38), residues: 204 loop : -1.37 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 64 TYR 0.061 0.004 TYR B 342 PHE 0.034 0.004 PHE A 87 TRP 0.052 0.006 TRP B 21 HIS 0.015 0.003 HIS K 100 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 9741) covalent geometry : angle 1.11806 (13221) hydrogen bonds : bond 0.05672 ( 402) hydrogen bonds : angle 5.69963 ( 1182) Misc. bond : bond 0.00176 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 SER cc_start: 0.8356 (p) cc_final: 0.7952 (p) REVERT: B 269 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7338 (ptm) REVERT: B 380 ASN cc_start: 0.7050 (t0) cc_final: 0.6538 (t160) REVERT: B 393 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8019 (tm-30) REVERT: B 400 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7286 (tmt170) REVERT: B 422 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6582 (tp30) REVERT: B 431 GLU cc_start: 0.7348 (pp20) cc_final: 0.7029 (pp20) REVERT: B 433 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7410 (tp-100) REVERT: K 8 ASN cc_start: 0.8051 (p0) cc_final: 0.7827 (p0) REVERT: K 15 PHE cc_start: 0.7707 (m-80) cc_final: 0.7109 (m-80) REVERT: K 101 ASP cc_start: 0.7669 (t70) cc_final: 0.7331 (t0) REVERT: K 131 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6814 (tppp) REVERT: K 157 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6122 (tp30) REVERT: K 197 MET cc_start: 0.8042 (mpp) cc_final: 0.7839 (mpp) REVERT: K 250 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: K 297 THR cc_start: 0.8412 (p) cc_final: 0.8146 (t) REVERT: K 326 LYS cc_start: 0.8247 (mttt) cc_final: 0.7965 (mmpt) REVERT: A 2 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.5331 (mmt180) REVERT: A 176 GLN cc_start: 0.8542 (mm110) cc_final: 0.8123 (mm110) REVERT: A 377 MET cc_start: 0.5529 (ptm) cc_final: 0.4930 (pmm) REVERT: A 393 HIS cc_start: 0.7848 (t70) cc_final: 0.7634 (t-90) REVERT: A 408 TYR cc_start: 0.8231 (m-80) cc_final: 0.7960 (m-80) outliers start: 69 outliers final: 20 residues processed: 317 average time/residue: 0.4463 time to fit residues: 153.9944 Evaluate side-chains 223 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 157 GLU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS B 50 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN K 211 ASN A 8 HIS A 101 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.117063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102046 restraints weight = 19165.317| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.60 r_work: 0.3380 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 1.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9742 Z= 0.159 Angle : 0.793 11.249 13221 Z= 0.387 Chirality : 0.047 0.219 1458 Planarity : 0.005 0.048 1708 Dihedral : 11.814 142.534 1460 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.45 % Allowed : 27.01 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.52 (0.23), residues: 1184 helix: 0.35 (0.22), residues: 484 sheet: -0.18 (0.37), residues: 199 loop : -1.02 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.018 0.002 TYR B 185 PHE 0.028 0.002 PHE K 318 TRP 0.026 0.002 TRP A 21 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9741) covalent geometry : angle 0.79284 (13221) hydrogen bonds : bond 0.04006 ( 402) hydrogen bonds : angle 4.73831 ( 1182) Misc. bond : bond 0.00228 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7711 (ptp-110) REVERT: B 218 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8339 (mmmm) REVERT: B 235 MET cc_start: 0.7228 (tmm) cc_final: 0.6415 (ttm) REVERT: B 269 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7084 (tmt) REVERT: B 293 GLN cc_start: 0.7505 (tt0) cc_final: 0.6980 (tp40) REVERT: B 306 ASP cc_start: 0.7993 (p0) cc_final: 0.7586 (p0) REVERT: B 371 LEU cc_start: 0.7083 (mt) cc_final: 0.6696 (mm) REVERT: B 393 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 400 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7431 (tmt170) REVERT: B 422 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6546 (tp30) REVERT: B 431 GLU cc_start: 0.7438 (pp20) cc_final: 0.7186 (pp20) REVERT: K 53 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6840 (tm-30) REVERT: K 131 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6580 (tppp) REVERT: K 277 TYR cc_start: 0.8049 (m-80) cc_final: 0.7722 (m-80) REVERT: K 282 MET cc_start: 0.8061 (mmp) cc_final: 0.7758 (mmm) REVERT: K 297 THR cc_start: 0.8382 (p) cc_final: 0.8111 (t) REVERT: K 326 LYS cc_start: 0.8383 (mttt) cc_final: 0.8010 (mmpt) REVERT: A 2 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.4709 (mmt180) REVERT: A 112 LYS cc_start: 0.7976 (tptp) cc_final: 0.6947 (ttpp) REVERT: A 176 GLN cc_start: 0.8464 (mm110) cc_final: 0.8032 (mm110) REVERT: A 280 LYS cc_start: 0.6410 (mtmm) cc_final: 0.6102 (mmtp) outliers start: 46 outliers final: 21 residues processed: 267 average time/residue: 0.4555 time to fit residues: 132.1654 Evaluate side-chains 227 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 50 ASN B 186 ASN B 249 ASN B 380 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100061 restraints weight = 19460.572| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.61 r_work: 0.3368 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 1.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9742 Z= 0.182 Angle : 0.809 9.907 13221 Z= 0.399 Chirality : 0.048 0.238 1458 Planarity : 0.005 0.046 1708 Dihedral : 11.514 133.836 1460 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.16 % Allowed : 28.46 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.44 (0.23), residues: 1184 helix: 0.48 (0.23), residues: 486 sheet: -0.16 (0.37), residues: 198 loop : -1.04 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.014 0.002 TYR A 312 PHE 0.024 0.002 PHE K 318 TRP 0.031 0.002 TRP A 21 HIS 0.035 0.002 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9741) covalent geometry : angle 0.80855 (13221) hydrogen bonds : bond 0.03950 ( 402) hydrogen bonds : angle 4.54510 ( 1182) Misc. bond : bond 0.00366 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.5506 (t70) REVERT: B 50 ASN cc_start: 0.8847 (m-40) cc_final: 0.8305 (t0) REVERT: B 51 VAL cc_start: 0.9388 (t) cc_final: 0.9171 (p) REVERT: B 123 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7910 (ptp-110) REVERT: B 166 MET cc_start: 0.5622 (tpp) cc_final: 0.5326 (mmm) REVERT: B 218 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8526 (mmmm) REVERT: B 235 MET cc_start: 0.7173 (tmm) cc_final: 0.6817 (ttm) REVERT: B 247 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8670 (mt0) REVERT: B 293 GLN cc_start: 0.7530 (tt0) cc_final: 0.7090 (tp40) REVERT: B 325 MET cc_start: 0.7652 (mpt) cc_final: 0.7327 (mpt) REVERT: B 393 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 422 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6760 (tp30) REVERT: K 131 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7211 (tppp) REVERT: K 185 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8543 (mm-30) REVERT: K 277 TYR cc_start: 0.8261 (m-80) cc_final: 0.7956 (m-80) REVERT: K 326 LYS cc_start: 0.8572 (mttt) cc_final: 0.8248 (ttmm) REVERT: A 2 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5209 (mmt180) REVERT: A 21 TRP cc_start: 0.5704 (OUTLIER) cc_final: 0.4586 (m-10) REVERT: A 90 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8407 (mp0) REVERT: A 97 GLU cc_start: 0.8816 (mp0) cc_final: 0.8359 (mp0) REVERT: A 112 LYS cc_start: 0.8640 (tptp) cc_final: 0.7996 (ttpt) REVERT: A 176 GLN cc_start: 0.8490 (mm110) cc_final: 0.8071 (mm110) REVERT: A 230 LEU cc_start: 0.8963 (mm) cc_final: 0.8643 (tm) REVERT: A 234 ILE cc_start: 0.7863 (mt) cc_final: 0.7573 (mt) REVERT: A 280 LYS cc_start: 0.7224 (mtmm) cc_final: 0.6834 (mmtp) REVERT: A 377 MET cc_start: 0.6533 (ptt) cc_final: 0.6252 (pmt) outliers start: 43 outliers final: 21 residues processed: 259 average time/residue: 0.4650 time to fit residues: 131.0797 Evaluate side-chains 232 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 103 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN B 350 ASN ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098462 restraints weight = 19663.236| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.70 r_work: 0.3334 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 1.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9742 Z= 0.147 Angle : 0.792 10.199 13221 Z= 0.384 Chirality : 0.046 0.179 1458 Planarity : 0.005 0.081 1708 Dihedral : 11.161 136.404 1460 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.48 % Allowed : 30.40 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.31 (0.23), residues: 1184 helix: 0.63 (0.22), residues: 492 sheet: -0.32 (0.35), residues: 198 loop : -0.92 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 400 TYR 0.021 0.001 TYR B 185 PHE 0.024 0.002 PHE K 128 TRP 0.027 0.002 TRP A 21 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9741) covalent geometry : angle 0.79178 (13221) hydrogen bonds : bond 0.03693 ( 402) hydrogen bonds : angle 4.45585 ( 1182) Misc. bond : bond 0.00631 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.380 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: B 28 HIS cc_start: 0.6354 (OUTLIER) cc_final: 0.5694 (t70) REVERT: B 50 ASN cc_start: 0.8782 (m-40) cc_final: 0.8152 (t160) REVERT: B 70 LEU cc_start: 0.7067 (mt) cc_final: 0.6635 (mm) REVERT: B 91 ASN cc_start: 0.7781 (m-40) cc_final: 0.7575 (m-40) REVERT: B 105 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7759 (tppp) REVERT: B 166 MET cc_start: 0.6350 (tpp) cc_final: 0.6028 (mmm) REVERT: B 218 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8544 (mmmm) REVERT: B 235 MET cc_start: 0.7415 (tmm) cc_final: 0.7085 (ttm) REVERT: B 269 MET cc_start: 0.6861 (ptm) cc_final: 0.6566 (ptp) REVERT: B 293 GLN cc_start: 0.7505 (tt0) cc_final: 0.7125 (tp40) REVERT: B 325 MET cc_start: 0.7347 (mpt) cc_final: 0.7135 (mpp) REVERT: B 393 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 422 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6842 (tp30) REVERT: K 131 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7315 (tppp) REVERT: K 137 ILE cc_start: 0.9072 (mp) cc_final: 0.8854 (mm) REVERT: K 277 TYR cc_start: 0.8336 (m-80) cc_final: 0.7666 (m-80) REVERT: K 282 MET cc_start: 0.8378 (mmm) cc_final: 0.8009 (mmm) REVERT: K 326 LYS cc_start: 0.8592 (mttt) cc_final: 0.8316 (ttmm) REVERT: A 2 ARG cc_start: 0.6495 (OUTLIER) cc_final: 0.5490 (mmt180) REVERT: A 15 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: A 21 TRP cc_start: 0.6001 (OUTLIER) cc_final: 0.5115 (m-10) REVERT: A 97 GLU cc_start: 0.8831 (mp0) cc_final: 0.8566 (mp0) REVERT: A 112 LYS cc_start: 0.8802 (tptp) cc_final: 0.8121 (mtpm) REVERT: A 113 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7206 (mp0) REVERT: A 150 THR cc_start: 0.9009 (m) cc_final: 0.8695 (t) REVERT: A 176 GLN cc_start: 0.8567 (mm110) cc_final: 0.8182 (mm110) REVERT: A 230 LEU cc_start: 0.8959 (mm) cc_final: 0.8638 (tm) REVERT: A 280 LYS cc_start: 0.7323 (mtmm) cc_final: 0.6893 (mmtp) REVERT: A 302 MET cc_start: 0.6719 (tmm) cc_final: 0.6487 (ttm) REVERT: A 377 MET cc_start: 0.6267 (ptt) cc_final: 0.5956 (pmt) outliers start: 36 outliers final: 16 residues processed: 253 average time/residue: 0.4268 time to fit residues: 118.3452 Evaluate side-chains 227 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN K 221 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095998 restraints weight = 19975.384| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.67 r_work: 0.3306 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 1.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9742 Z= 0.184 Angle : 0.838 16.351 13221 Z= 0.406 Chirality : 0.048 0.274 1458 Planarity : 0.005 0.045 1708 Dihedral : 10.702 134.396 1460 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.29 % Allowed : 33.40 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.35 (0.23), residues: 1184 helix: 0.59 (0.22), residues: 494 sheet: -0.27 (0.36), residues: 188 loop : -0.96 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.049 0.002 TYR A 357 PHE 0.017 0.002 PHE K 318 TRP 0.039 0.002 TRP A 21 HIS 0.015 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9741) covalent geometry : angle 0.83837 (13221) hydrogen bonds : bond 0.03751 ( 402) hydrogen bonds : angle 4.45942 ( 1182) Misc. bond : bond 0.01175 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.395 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: B 60 LYS cc_start: 0.7323 (mmmt) cc_final: 0.7108 (ttpt) REVERT: B 75 MET cc_start: 0.7693 (ppp) cc_final: 0.7380 (mtp) REVERT: B 83 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7463 (t80) REVERT: B 119 LEU cc_start: 0.8653 (tt) cc_final: 0.8274 (mt) REVERT: B 131 CYS cc_start: 0.6362 (t) cc_final: 0.5427 (t) REVERT: B 218 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8697 (mmmm) REVERT: B 269 MET cc_start: 0.7064 (ptm) cc_final: 0.6859 (ptp) REVERT: B 293 GLN cc_start: 0.7648 (tt0) cc_final: 0.7290 (tp40) REVERT: B 332 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.7034 (mtm) REVERT: B 373 MET cc_start: 0.6109 (ptt) cc_final: 0.5582 (pmt) REVERT: B 393 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 422 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7026 (tp30) REVERT: K 12 MET cc_start: 0.7249 (ppp) cc_final: 0.6839 (pmm) REVERT: K 131 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7521 (tppp) REVERT: K 137 ILE cc_start: 0.9237 (mp) cc_final: 0.9001 (mm) REVERT: K 168 CYS cc_start: 0.8453 (t) cc_final: 0.8197 (p) REVERT: K 170 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8107 (mt-10) REVERT: K 184 ASP cc_start: 0.9031 (t0) cc_final: 0.8806 (p0) REVERT: K 244 GLU cc_start: 0.7261 (pp20) cc_final: 0.6982 (pm20) REVERT: K 277 TYR cc_start: 0.8450 (m-80) cc_final: 0.8054 (m-80) REVERT: K 282 MET cc_start: 0.8438 (mmm) cc_final: 0.8137 (mmm) REVERT: A 2 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5693 (mmt180) REVERT: A 21 TRP cc_start: 0.6622 (OUTLIER) cc_final: 0.5678 (m-10) REVERT: A 22 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7252 (mm-30) REVERT: A 112 LYS cc_start: 0.8822 (tptp) cc_final: 0.8377 (mtpm) REVERT: A 113 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7670 (mp0) REVERT: A 176 GLN cc_start: 0.8803 (mm110) cc_final: 0.8531 (mm110) REVERT: A 230 LEU cc_start: 0.9081 (mm) cc_final: 0.8758 (tm) REVERT: A 280 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7213 (mmtt) REVERT: A 301 GLN cc_start: 0.7631 (tp-100) cc_final: 0.6955 (mm110) REVERT: A 377 MET cc_start: 0.6762 (ptt) cc_final: 0.6515 (pmt) outliers start: 34 outliers final: 17 residues processed: 254 average time/residue: 0.4317 time to fit residues: 119.8720 Evaluate side-chains 238 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 221 GLN Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN K 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094324 restraints weight = 19987.903| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.64 r_work: 0.3301 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 1.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9742 Z= 0.154 Angle : 0.858 13.247 13221 Z= 0.410 Chirality : 0.048 0.173 1458 Planarity : 0.005 0.064 1708 Dihedral : 10.491 135.411 1460 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.61 % Allowed : 35.62 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.22 (0.24), residues: 1184 helix: 0.65 (0.23), residues: 495 sheet: -0.26 (0.36), residues: 194 loop : -0.83 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 215 TYR 0.023 0.002 TYR B 185 PHE 0.023 0.002 PHE K 318 TRP 0.035 0.002 TRP A 21 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9741) covalent geometry : angle 0.85809 (13221) hydrogen bonds : bond 0.03879 ( 402) hydrogen bonds : angle 4.57461 ( 1182) Misc. bond : bond 0.00259 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.372 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: B 19 LYS cc_start: 0.8532 (tptp) cc_final: 0.8249 (tppp) REVERT: B 60 LYS cc_start: 0.7394 (mmmt) cc_final: 0.7119 (ttpt) REVERT: B 75 MET cc_start: 0.7714 (ppp) cc_final: 0.7365 (mtp) REVERT: B 110 GLU cc_start: 0.8820 (tp30) cc_final: 0.8498 (mm-30) REVERT: B 119 LEU cc_start: 0.8695 (tt) cc_final: 0.8376 (mt) REVERT: B 218 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8614 (mmmm) REVERT: B 269 MET cc_start: 0.7221 (ptm) cc_final: 0.6950 (ptp) REVERT: B 293 GLN cc_start: 0.7648 (tt0) cc_final: 0.7313 (tp40) REVERT: B 315 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8048 (t) REVERT: B 325 MET cc_start: 0.7465 (mpp) cc_final: 0.6710 (mpt) REVERT: B 332 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.7013 (mtm) REVERT: B 373 MET cc_start: 0.6377 (ptt) cc_final: 0.5813 (pmt) REVERT: B 393 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 398 MET cc_start: 0.8129 (tmm) cc_final: 0.4713 (mmp) REVERT: B 433 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7652 (tp-100) REVERT: K 12 MET cc_start: 0.7389 (ppp) cc_final: 0.6997 (pmm) REVERT: K 131 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7534 (tppp) REVERT: K 180 MET cc_start: 0.8341 (mmt) cc_final: 0.8108 (mmp) REVERT: K 244 GLU cc_start: 0.7384 (pp20) cc_final: 0.7156 (pm20) REVERT: K 277 TYR cc_start: 0.8418 (m-80) cc_final: 0.8181 (m-80) REVERT: K 282 MET cc_start: 0.8351 (mmm) cc_final: 0.8106 (mmm) REVERT: A 1 MET cc_start: 0.8135 (pmm) cc_final: 0.7761 (ppp) REVERT: A 2 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6019 (mmt180) REVERT: A 21 TRP cc_start: 0.6780 (OUTLIER) cc_final: 0.5863 (m-10) REVERT: A 22 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7406 (mm-30) REVERT: A 112 LYS cc_start: 0.8800 (tptp) cc_final: 0.8386 (mtpm) REVERT: A 113 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7785 (mp0) REVERT: A 128 GLN cc_start: 0.8837 (mm110) cc_final: 0.8574 (mp10) REVERT: A 176 GLN cc_start: 0.8839 (mm110) cc_final: 0.8629 (mm110) REVERT: A 230 LEU cc_start: 0.9106 (mm) cc_final: 0.8810 (tm) REVERT: A 280 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7026 (mmtm) outliers start: 27 outliers final: 17 residues processed: 252 average time/residue: 0.4253 time to fit residues: 117.3726 Evaluate side-chains 243 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 221 GLN Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN ** K 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 HIS ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.104760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.088595 restraints weight = 19937.694| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.59 r_work: 0.3205 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 1.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9742 Z= 0.205 Angle : 0.926 14.338 13221 Z= 0.448 Chirality : 0.052 0.404 1458 Planarity : 0.006 0.053 1708 Dihedral : 10.372 135.247 1460 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.10 % Allowed : 35.53 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.41 (0.23), residues: 1184 helix: 0.38 (0.22), residues: 501 sheet: -0.28 (0.37), residues: 185 loop : -0.83 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 215 TYR 0.022 0.002 TYR B 185 PHE 0.019 0.002 PHE K 318 TRP 0.046 0.002 TRP A 21 HIS 0.005 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9741) covalent geometry : angle 0.92571 (13221) hydrogen bonds : bond 0.04356 ( 402) hydrogen bonds : angle 4.69400 ( 1182) Misc. bond : bond 0.00317 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.403 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 60 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7533 (ttpt) REVERT: B 86 ILE cc_start: 0.9346 (tp) cc_final: 0.9115 (mm) REVERT: B 325 MET cc_start: 0.7876 (mpp) cc_final: 0.7511 (mpp) REVERT: B 393 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 398 MET cc_start: 0.8361 (tmm) cc_final: 0.4940 (mmt) REVERT: B 433 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8182 (tm-30) REVERT: K 58 GLN cc_start: 0.6418 (pm20) cc_final: 0.5813 (mt0) REVERT: K 131 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7875 (tppp) REVERT: A 1 MET cc_start: 0.8119 (pmm) cc_final: 0.7866 (ppp) REVERT: A 2 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6560 (mmt180) REVERT: A 22 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7719 (tt0) REVERT: A 52 PHE cc_start: 0.8785 (m-80) cc_final: 0.8581 (m-10) REVERT: A 98 ASP cc_start: 0.8882 (p0) cc_final: 0.8340 (p0) REVERT: A 112 LYS cc_start: 0.8858 (tptp) cc_final: 0.8537 (mtmt) REVERT: A 113 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8011 (mp0) REVERT: A 123 ARG cc_start: 0.9053 (ppp80) cc_final: 0.8835 (tmm-80) REVERT: A 155 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8486 (pp20) REVERT: A 211 ASP cc_start: 0.8193 (m-30) cc_final: 0.7777 (m-30) REVERT: A 214 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7984 (ttp80) REVERT: A 269 LEU cc_start: 0.8916 (pp) cc_final: 0.8672 (pp) REVERT: A 271 THR cc_start: 0.7244 (m) cc_final: 0.6946 (p) REVERT: A 379 SER cc_start: 0.8705 (m) cc_final: 0.8268 (p) REVERT: A 414 GLU cc_start: 0.7523 (pp20) cc_final: 0.7315 (pp20) outliers start: 32 outliers final: 15 residues processed: 261 average time/residue: 0.4793 time to fit residues: 136.1952 Evaluate side-chains 224 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 177 VAL 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 252 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 431 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 ASN K 129 HIS K 221 GLN A 176 GLN A 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.105212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089892 restraints weight = 20802.396| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.65 r_work: 0.3216 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 1.8184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9742 Z= 0.156 Angle : 0.871 13.521 13221 Z= 0.421 Chirality : 0.050 0.345 1458 Planarity : 0.005 0.056 1708 Dihedral : 10.275 137.199 1460 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.42 % Allowed : 38.33 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.20 (0.23), residues: 1184 helix: 0.54 (0.22), residues: 499 sheet: -0.00 (0.37), residues: 182 loop : -0.76 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 215 TYR 0.021 0.002 TYR B 185 PHE 0.023 0.002 PHE K 318 TRP 0.025 0.002 TRP A 21 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9741) covalent geometry : angle 0.87116 (13221) hydrogen bonds : bond 0.03979 ( 402) hydrogen bonds : angle 4.72069 ( 1182) Misc. bond : bond 0.00261 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3302.73 seconds wall clock time: 57 minutes 16.94 seconds (3436.94 seconds total)