Starting phenix.real_space_refine on Sun Dec 29 01:02:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhb_19174/12_2024/8rhb_19174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhb_19174/12_2024/8rhb_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_19174/12_2024/8rhb_19174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhb_19174/12_2024/8rhb_19174.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhb_19174/12_2024/8rhb_19174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhb_19174/12_2024/8rhb_19174.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.18, per 1000 atoms: 0.65 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.84 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: 2.69 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 0.940 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- 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 : 0.005 0.175 9741 Z= 0.322 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), 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 TRP 0.010 0.001 TRP A 346 HIS 0.003 0.001 HIS K 129 PHE 0.017 0.001 PHE K 82 TYR 0.011 0.001 TYR B 161 ARG 0.001 0.000 ARG K 25 *********************** 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 : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6696 (tm-30) outliers start: 0 outliers final: 2 residues processed: 275 average time/residue: 1.2119 time to fit residues: 358.0213 Evaluate side-chains 147 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 35 optimal weight: 0.0170 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- 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 93 HIS K 129 HIS K 211 ASN K 327 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3637 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9741 Z= 0.218 Angle : 0.750 16.118 13221 Z= 0.364 Chirality : 0.046 0.240 1458 Planarity : 0.005 0.082 1708 Dihedral : 15.695 174.525 1465 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.36 % Allowed : 18.59 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1184 helix: 1.34 (0.23), residues: 480 sheet: -0.24 (0.36), residues: 212 loop : -1.02 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 21 HIS 0.025 0.002 HIS B 28 PHE 0.012 0.001 PHE B 20 TYR 0.022 0.002 TYR A 103 ARG 0.014 0.001 ARG B 278 *********************** 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 206 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 1.015 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 393 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6595 (tm-30) REVERT: A 80 THR cc_start: 0.6265 (OUTLIER) cc_final: 0.6038 (p) outliers start: 45 outliers final: 9 residues processed: 193 average time/residue: 0.9620 time to fit residues: 202.6342 Evaluate side-chains 140 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 165 VAL 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 59 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 206 ASN B 293 GLN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN K 34 GLN K 129 HIS K 214 GLN A 18 ASN A 101 ASN A 176 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4607 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9741 Z= 0.286 Angle : 0.796 11.473 13221 Z= 0.396 Chirality : 0.047 0.259 1458 Planarity : 0.006 0.063 1708 Dihedral : 12.363 178.603 1460 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 4.26 % Allowed : 17.81 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1184 helix: 0.65 (0.22), residues: 491 sheet: 0.00 (0.38), residues: 198 loop : -1.02 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 21 HIS 0.022 0.002 HIS B 28 PHE 0.016 0.002 PHE A 404 TYR 0.023 0.002 TYR A 408 ARG 0.014 0.001 ARG B 264 *********************** 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 216 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.038 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 52 TYR cc_start: 0.5564 (m-80) cc_final: 0.5331 (m-80) REVERT: B 393 GLU cc_start: 0.7306 (tm-30) cc_final: 0.7044 (tm-30) outliers start: 44 outliers final: 15 residues processed: 204 average time/residue: 1.0963 time to fit residues: 241.3963 Evaluate side-chains 166 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 146 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 297 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN K 125 ASN K 129 HIS K 189 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.8741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 9741 Z= 0.355 Angle : 0.835 13.050 13221 Z= 0.424 Chirality : 0.049 0.300 1458 Planarity : 0.006 0.107 1708 Dihedral : 12.233 165.215 1460 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.74 % Allowed : 18.97 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1184 helix: 0.85 (0.23), residues: 473 sheet: -0.01 (0.38), residues: 201 loop : -1.03 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 21 HIS 0.011 0.002 HIS A 8 PHE 0.022 0.002 PHE A 67 TYR 0.025 0.002 TYR A 224 ARG 0.007 0.001 ARG B 311 *********************** 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 280 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.109 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 393 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7455 (tm-30) REVERT: K 180 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5743 (tpt) REVERT: A 296 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4734 (m-80) REVERT: A 377 MET cc_start: 0.3920 (ptm) cc_final: 0.3530 (pmm) outliers start: 49 outliers final: 17 residues processed: 261 average time/residue: 0.9335 time to fit residues: 266.1740 Evaluate side-chains 182 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 300 ILE Chi-restraints excluded: chain A residue 21 TRP Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 171 ILE 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 219 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 296 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN K 216 ASN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 1.0262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9741 Z= 0.272 Angle : 0.772 9.965 13221 Z= 0.387 Chirality : 0.048 0.227 1458 Planarity : 0.005 0.080 1708 Dihedral : 11.732 151.001 1460 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.68 % Allowed : 26.33 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1184 helix: 0.83 (0.22), residues: 484 sheet: 0.04 (0.37), residues: 195 loop : -0.92 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 346 HIS 0.010 0.001 HIS A 8 PHE 0.023 0.002 PHE B 377 TYR 0.036 0.002 TYR A 103 ARG 0.006 0.001 ARG B 123 *********************** 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 244 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.037 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 247 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7564 (mm-40) REVERT: B 393 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7315 (tm-30) REVERT: K 180 MET cc_start: 0.6548 (pp-130) cc_final: 0.6183 (tpt) outliers start: 38 outliers final: 20 residues processed: 230 average time/residue: 0.8503 time to fit residues: 216.0361 Evaluate side-chains 194 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 195 THR 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 21 TRP 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 219 ILE Chi-restraints excluded: chain A residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 1.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9741 Z= 0.239 Angle : 0.768 11.807 13221 Z= 0.377 Chirality : 0.047 0.218 1458 Planarity : 0.005 0.049 1708 Dihedral : 11.097 133.623 1460 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.74 % Allowed : 26.62 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1184 helix: 0.98 (0.23), residues: 491 sheet: 0.05 (0.37), residues: 195 loop : -0.81 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 21 HIS 0.008 0.001 HIS B 28 PHE 0.026 0.002 PHE K 128 TYR 0.021 0.002 TYR B 408 ARG 0.006 0.001 ARG B 123 *********************** 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 248 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.129 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 247 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7822 (mt0) REVERT: B 377 PHE cc_start: 0.7095 (t80) cc_final: 0.6420 (t80) REVERT: B 393 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 433 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6469 (tp-100) REVERT: A 112 LYS cc_start: 0.7833 (tptp) cc_final: 0.7169 (ttpp) REVERT: A 203 MET cc_start: 0.6053 (mmm) cc_final: 0.5470 (mmm) REVERT: A 377 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.4335 (pmt) outliers start: 49 outliers final: 22 residues processed: 232 average time/residue: 0.8525 time to fit residues: 217.7330 Evaluate side-chains 210 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 158 SER 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 219 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 350 ASN K 129 HIS K 211 ASN K 214 GLN ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 308 ASN A 176 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 1.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 9741 Z= 0.380 Angle : 0.968 14.143 13221 Z= 0.497 Chirality : 0.055 0.306 1458 Planarity : 0.006 0.072 1708 Dihedral : 11.000 139.747 1460 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 4.26 % Allowed : 28.27 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1184 helix: 0.44 (0.22), residues: 500 sheet: -0.27 (0.34), residues: 197 loop : -0.95 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 21 HIS 0.018 0.002 HIS B 229 PHE 0.033 0.003 PHE K 82 TYR 0.036 0.003 TYR B 185 ARG 0.006 0.001 ARG B 243 *********************** 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 324 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.905 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: B 50 ASN cc_start: 0.8509 (t0) cc_final: 0.8175 (t0) REVERT: B 75 MET cc_start: 0.7274 (ppp) cc_final: 0.6905 (mtp) REVERT: B 83 PHE cc_start: 0.7366 (m-80) cc_final: 0.7094 (t80) REVERT: B 166 MET cc_start: 0.6858 (tpt) cc_final: 0.6577 (mmt) REVERT: B 248 LEU cc_start: 0.9521 (tp) cc_final: 0.9305 (tp) REVERT: B 288 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6979 (t) REVERT: B 302 MET cc_start: 0.4845 (ttp) cc_final: 0.4631 (ttm) REVERT: B 393 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 433 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6724 (tp-100) REVERT: K 12 MET cc_start: 0.6475 (ppp) cc_final: 0.6135 (ptp) REVERT: A 70 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6521 (mm) REVERT: A 230 LEU cc_start: 0.8977 (mm) cc_final: 0.8757 (tm) outliers start: 44 outliers final: 13 residues processed: 308 average time/residue: 0.9324 time to fit residues: 313.1210 Evaluate side-chains 233 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ARG 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 288 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS B 167 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN B 380 ASN K 125 ASN K 211 ASN ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 1.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9741 Z= 0.239 Angle : 0.829 11.489 13221 Z= 0.408 Chirality : 0.048 0.191 1458 Planarity : 0.005 0.049 1708 Dihedral : 10.541 137.846 1460 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.87 % Allowed : 33.49 % Favored : 62.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.23), residues: 1184 helix: 0.67 (0.22), residues: 499 sheet: -0.08 (0.36), residues: 185 loop : -0.89 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 21 HIS 0.010 0.001 HIS B 229 PHE 0.020 0.002 PHE K 82 TYR 0.025 0.002 TYR K 84 ARG 0.009 0.001 ARG B 243 *********************** 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 272 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.065 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 50 ASN cc_start: 0.8546 (t0) cc_final: 0.8264 (t0) REVERT: B 70 LEU cc_start: 0.7509 (mp) cc_final: 0.6954 (mt) REVERT: B 196 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7384 (tm-30) REVERT: B 197 ASN cc_start: 0.7649 (m-40) cc_final: 0.7248 (m-40) REVERT: B 293 GLN cc_start: 0.7543 (tt0) cc_final: 0.7212 (tp40) REVERT: B 315 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7612 (t) REVERT: B 325 MET cc_start: 0.7798 (mpt) cc_final: 0.7032 (mpt) REVERT: B 393 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7271 (tm-30) REVERT: B 433 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6781 (tp-100) REVERT: K 170 GLU cc_start: 0.7262 (tp30) cc_final: 0.7025 (mm-30) REVERT: A 113 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7589 (mp0) REVERT: A 211 ASP cc_start: 0.7467 (m-30) cc_final: 0.7254 (m-30) REVERT: A 230 LEU cc_start: 0.8997 (mm) cc_final: 0.8747 (tm) REVERT: A 234 ILE cc_start: 0.8331 (mt) cc_final: 0.8003 (mt) REVERT: A 269 LEU cc_start: 0.8144 (pt) cc_final: 0.7828 (pp) REVERT: A 394 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6712 (ttpt) outliers start: 40 outliers final: 19 residues processed: 253 average time/residue: 0.9712 time to fit residues: 268.6981 Evaluate side-chains 239 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 167 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain A residue 4 CYS 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 224 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 394 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** K 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 1.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9741 Z= 0.267 Angle : 0.903 14.459 13221 Z= 0.446 Chirality : 0.050 0.317 1458 Planarity : 0.005 0.049 1708 Dihedral : 10.363 137.964 1460 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 34.27 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1184 helix: 0.56 (0.22), residues: 501 sheet: -0.18 (0.35), residues: 204 loop : -0.79 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.010 0.001 HIS B 28 PHE 0.023 0.002 PHE B 83 TYR 0.024 0.002 TYR A 224 ARG 0.012 0.001 ARG B 2 *********************** 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 265 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.094 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 50 ASN cc_start: 0.8625 (t0) cc_final: 0.8349 (t160) REVERT: B 83 PHE cc_start: 0.7726 (m-80) cc_final: 0.7478 (t80) REVERT: B 247 GLN cc_start: 0.8482 (mt0) cc_final: 0.8232 (mm-40) REVERT: B 293 GLN cc_start: 0.7570 (tt0) cc_final: 0.7296 (tp40) REVERT: B 315 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8178 (t) REVERT: B 393 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 433 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6926 (tp-100) REVERT: K 131 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7679 (ttpt) REVERT: K 157 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6455 (tm-30) REVERT: A 98 ASP cc_start: 0.8508 (p0) cc_final: 0.8148 (p0) REVERT: A 155 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8267 (pp20) REVERT: A 172 TYR cc_start: 0.6393 (t80) cc_final: 0.6146 (t80) REVERT: A 211 ASP cc_start: 0.7586 (m-30) cc_final: 0.7373 (m-30) REVERT: A 230 LEU cc_start: 0.9111 (mm) cc_final: 0.8902 (tm) outliers start: 35 outliers final: 16 residues processed: 245 average time/residue: 0.9419 time to fit residues: 254.3378 Evaluate side-chains 230 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL 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 324 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 1.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9741 Z= 0.263 Angle : 0.885 11.405 13221 Z= 0.431 Chirality : 0.049 0.289 1458 Planarity : 0.005 0.050 1708 Dihedral : 10.253 138.751 1460 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.42 % Allowed : 37.56 % Favored : 60.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1184 helix: 0.66 (0.23), residues: 499 sheet: -0.32 (0.35), residues: 210 loop : -0.86 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.007 0.001 HIS A 197 PHE 0.018 0.002 PHE K 82 TYR 0.021 0.002 TYR A 224 ARG 0.009 0.001 ARG A 215 ********************** 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 254 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 1.065 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 50 ASN cc_start: 0.8652 (t0) cc_final: 0.8417 (t160) REVERT: B 149 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8916 (mmm) REVERT: B 293 GLN cc_start: 0.7473 (tt0) cc_final: 0.7268 (tp40) REVERT: B 315 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8397 (t) REVERT: B 372 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7812 (pttm) REVERT: B 393 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 433 GLN cc_start: 0.7560 (mm-40) cc_final: 0.6983 (tp-100) REVERT: A 98 ASP cc_start: 0.8595 (p0) cc_final: 0.8280 (p0) REVERT: A 155 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8294 (pp20) REVERT: A 271 THR cc_start: 0.7177 (m) cc_final: 0.6796 (p) outliers start: 25 outliers final: 16 residues processed: 243 average time/residue: 0.9294 time to fit residues: 246.9775 Evaluate side-chains 222 residues out of total 1033 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 167 ASN 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 324 SER Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 128 PHE Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS B 167 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN K 117 ASN K 320 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 176 GLN A 216 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.109623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093816 restraints weight = 21595.720| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.81 r_work: 0.3281 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 1.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9741 Z= 0.244 Angle : 0.897 14.641 13221 Z= 0.436 Chirality : 0.049 0.279 1458 Planarity : 0.006 0.096 1708 Dihedral : 10.201 137.505 1460 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.32 % Allowed : 37.95 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1184 helix: 0.65 (0.23), residues: 502 sheet: -0.23 (0.35), residues: 209 loop : -0.90 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 21 HIS 0.005 0.001 HIS A 197 PHE 0.022 0.002 PHE B 83 TYR 0.022 0.001 TYR A 103 ARG 0.027 0.001 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4196.21 seconds wall clock time: 75 minutes 50.57 seconds (4550.57 seconds total)