Starting phenix.real_space_refine on Sun Jul 5 10:20:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9puv_71877/07_2026/9puv_71877.map" } resolution = 3.68 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= -0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians S 100 5.16 5 C 8449 2.51 5 N 2304 2.21 5 O 2475 1.98 5 H 12914 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26242 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12551 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 42, 'TRANS': 745} Chain breaks: 4 Chain: "B" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 556 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "C" Number of atoms: 12549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 12549 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 42, 'TRANS': 745} Chain breaks: 4 Chain: "D" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 586 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 4.45, per 1000 atoms: 0.17 Number of scatterers: 26242 At special positions: 0 Unit cell: (129.32, 150.52, 135.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 O 2475 8.00 N 2304 7.00 C 8449 6.00 H 12914 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 304 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 862 " distance=2.03 Simple disulfide: pdb=" SG CYS C 788 " - pdb=" SG CYS C 797 " distance=2.02 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 40 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 852.5 milliseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 33 sheets defined 15.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.702A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.990A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 193 through 200 removed outlier: 6.476A pdb=" N SER A 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 200 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.617A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.540A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.526A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.173A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.743A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 71 through 76 removed outlier: 4.527A pdb=" N LEU C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 193 through 200 removed outlier: 6.660A pdb=" N SER C 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.788A pdb=" N GLU C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.599A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 640 through 644 removed outlier: 3.668A pdb=" N LEU C 643 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 4.142A pdb=" N ASP C 814 " --> pdb=" O ALA C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 872 Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.621A pdb=" N TYR D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 removed outlier: 3.900A pdb=" N GLU D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 14 removed outlier: 6.890A pdb=" N GLU A 6 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU A 30 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 56 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 14 removed outlier: 6.890A pdb=" N GLU A 6 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU A 30 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU A 62 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 65 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 91 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.675A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321 removed outlier: 5.640A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 534 removed outlier: 4.528A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 506 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 567 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB3, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.524A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 636 through 637 removed outlier: 4.524A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB6, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB8, first strand: chain 'C' and resid 7 through 9 removed outlier: 6.619A pdb=" N CYS C 8 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 82 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 12 through 14 removed outlier: 7.206A pdb=" N GLN C 34 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 63 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 36 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG C 65 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 61 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE C 96 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 63 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG C 118 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 94 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU C 120 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 96 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 122 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 144 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN C 148 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AC2, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.507A pdb=" N HIS C 187 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 212 through 216 removed outlier: 3.516A pdb=" N ALA C 227 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN C 215 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS C 225 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'C' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'C' and resid 292 through 295 Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 342 removed outlier: 6.406A pdb=" N LEU C 340 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG C 371 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 342 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR C 398 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE C 427 " --> pdb=" O TYR C 398 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 400 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N HIS C 429 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 479 through 480 removed outlier: 3.981A pdb=" N LEU C 486 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 485 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 530 through 533 removed outlier: 3.556A pdb=" N THR C 530 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY C 502 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 571 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 604 through 609 removed outlier: 6.710A pdb=" N GLN C 612 " --> pdb=" O ASN C 608 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 762 through 765 removed outlier: 3.507A pdb=" N VAL C 632 " --> pdb=" O GLU C 762 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 764 " --> pdb=" O TYR C 630 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 821 through 824 Processing sheet with id=AD5, first strand: chain 'C' and resid 859 through 864 removed outlier: 3.597A pdb=" N LEU C 846 " --> pdb=" O THR C 891 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE C 888 " --> pdb=" O TRP C 899 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C 899 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA C 890 " --> pdb=" O GLY C 897 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 859 through 864 removed outlier: 3.597A pdb=" N LEU C 846 " --> pdb=" O THR C 891 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 831 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: 6.21 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12906 1.04 - 1.23: 465 1.23 - 1.43: 5418 1.43 - 1.63: 7661 1.63 - 1.83: 122 Bond restraints: 26572 Sorted by residual: bond pdb=" CA LEU A 434 " pdb=" CB LEU A 434 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.76e-02 3.23e+03 2.15e+00 bond pdb=" C ALA A 510 " pdb=" O ALA A 510 " ideal model delta sigma weight residual 1.249 1.238 0.011 8.50e-03 1.38e+04 1.70e+00 bond pdb=" N ILE A 587 " pdb=" CA ILE A 587 " ideal model delta sigma weight residual 1.474 1.454 0.020 1.57e-02 4.06e+03 1.62e+00 bond pdb=" CB CYS C 225 " pdb=" SG CYS C 225 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CA ASN A 298 " pdb=" CB ASN A 298 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.04e+00 ... (remaining 26567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 47239 1.58 - 3.16: 628 3.16 - 4.73: 51 4.73 - 6.31: 2 6.31 - 7.89: 1 Bond angle restraints: 47921 Sorted by residual: angle pdb=" N PHE C 88 " pdb=" CA PHE C 88 " pdb=" C PHE C 88 " ideal model delta sigma weight residual 110.80 105.93 4.87 2.13e+00 2.20e-01 5.22e+00 angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 113.19 109.60 3.59 1.58e+00 4.01e-01 5.17e+00 angle pdb=" CA LEU A 20 " pdb=" CB LEU A 20 " pdb=" CG LEU A 20 " ideal model delta sigma weight residual 116.30 124.19 -7.89 3.50e+00 8.16e-02 5.08e+00 angle pdb=" N SER A 296 " pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 113.19 110.59 2.60 1.19e+00 7.06e-01 4.78e+00 angle pdb=" C ASN A 298 " pdb=" CA ASN A 298 " pdb=" CB ASN A 298 " ideal model delta sigma weight residual 110.42 114.69 -4.27 1.99e+00 2.53e-01 4.60e+00 ... (remaining 47916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11067 17.55 - 35.10: 1146 35.10 - 52.65: 325 52.65 - 70.20: 74 70.20 - 87.76: 35 Dihedral angle restraints: 12647 sinusoidal: 6865 harmonic: 5782 Sorted by residual: dihedral pdb=" CB CYS C 241 " pdb=" SG CYS C 241 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 146.52 -53.52 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA LYS A 460 " pdb=" C LYS A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CB CYS A 435 " pdb=" SG CYS A 435 " pdb=" SG CYS A 468 " pdb=" CB CYS A 468 " ideal model delta sinusoidal sigma weight residual 93.00 52.35 40.65 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 12644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1243 0.030 - 0.060: 495 0.060 - 0.090: 99 0.090 - 0.120: 121 0.120 - 0.150: 33 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA ILE C 485 " pdb=" N ILE C 485 " pdb=" C ILE C 485 " pdb=" CB ILE C 485 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA VAL A 532 " pdb=" N VAL A 532 " pdb=" C VAL A 532 " pdb=" CB VAL A 532 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE A 534 " pdb=" N ILE A 534 " pdb=" C ILE A 534 " pdb=" CB ILE A 534 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1988 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 494 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO C 495 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 298 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C ASN A 298 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 298 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 431 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 432 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " -0.020 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1436 2.17 - 2.78: 52019 2.78 - 3.39: 72596 3.39 - 3.99: 94453 3.99 - 4.60: 144132 Nonbonded interactions: 364636 Sorted by model distance: nonbonded pdb=" O ILE C 55 " pdb=" H THR C 80 " model vdw 1.564 2.450 nonbonded pdb=" O ARG A 383 " pdb=" HE2 HIS A 417 " model vdw 1.569 2.450 nonbonded pdb=" O GLY A 161 " pdb=" H LYS A 166 " model vdw 1.582 2.450 nonbonded pdb=" H GLU C 453 " pdb=" OD2 ASP C 456 " model vdw 1.590 2.450 nonbonded pdb=" O THR A 595 " pdb="HD22 ASN A 789 " model vdw 1.592 2.450 ... (remaining 364631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 158 or (resid 159 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 160 through 181 or (resid 182 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 183 through 303 or (resid 304 and (name N or name CA or name C or name O or na \ me CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 305 thr \ ough 307 or (resid 308 and (name N or name CA or name C or name O or name CB or \ name SG or name H or name HA or name HB2 or name HB3)) or resid 309 through 909) \ ) selection = (chain 'C' and (resid 3 through 434 or (resid 435 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 436 through 467 or (resid 468 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 469 through 909)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 4 through 41) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.190 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.020 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13693 Z= 0.142 Angle : 0.534 7.888 18583 Z= 0.285 Chirality : 0.043 0.150 1991 Planarity : 0.003 0.052 2396 Dihedral : 16.076 87.756 5061 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.59 % Favored : 91.35 % Rotamer: Outliers : 0.27 % Allowed : 16.98 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.77 (0.21), residues: 1630 helix: -0.78 (0.39), residues: 166 sheet: -1.32 (0.28), residues: 369 loop : -1.20 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 13 TYR 0.011 0.001 TYR A 507 PHE 0.019 0.001 PHE A 567 TRP 0.009 0.001 TRP C 634 HIS 0.013 0.001 HIS A 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (13658) covalent geometry : angle 0.52956 / 0.28 (18513) SS BOND : bond 0.00304 / 0.18 ( 35) SS BOND : angle 1.25785 / 0.80 ( 70) hydrogen bonds : bond 0.24136 / 16.22 ( 315) hydrogen bonds : angle 9.93531 / 6.69 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5912 (m-70) outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.2854 time to fit residues: 39.2782 Evaluate side-chains 95 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.177202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.119306 restraints weight = 81333.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.123137 restraints weight = 53244.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124454 restraints weight = 34079.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.124679 restraints weight = 29956.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.125195 restraints weight = 29775.575| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13693 Z= 0.158 Angle : 0.557 4.794 18583 Z= 0.299 Chirality : 0.044 0.153 1991 Planarity : 0.004 0.050 2396 Dihedral : 4.946 56.670 1819 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.26 % Favored : 90.67 % Rotamer: Outliers : 1.61 % Allowed : 16.11 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.87 (0.21), residues: 1630 helix: -0.69 (0.39), residues: 170 sheet: -1.54 (0.28), residues: 361 loop : -1.25 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 371 TYR 0.014 0.001 TYR A 507 PHE 0.020 0.002 PHE A 567 TRP 0.009 0.001 TRP C 489 HIS 0.008 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (13658) covalent geometry : angle 0.55616 / 0.30 (18513) SS BOND : bond 0.00214 / 0.12 ( 35) SS BOND : angle 0.79882 / 0.51 ( 70) hydrogen bonds : bond 0.04937 / 3.40 ( 315) hydrogen bonds : angle 7.51511 / 5.09 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8666 (mt) outliers start: 24 outliers final: 16 residues processed: 116 average time/residue: 0.2877 time to fit residues: 48.0460 Evaluate side-chains 105 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS C 455 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.176506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116545 restraints weight = 80745.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122302 restraints weight = 44408.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123951 restraints weight = 30225.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.125145 restraints weight = 23138.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.125631 restraints weight = 21678.966| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13693 Z= 0.178 Angle : 0.544 5.221 18583 Z= 0.289 Chirality : 0.044 0.145 1991 Planarity : 0.004 0.049 2396 Dihedral : 4.875 55.605 1814 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.25 % Rotamer: Outliers : 2.15 % Allowed : 16.24 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.93 (0.21), residues: 1630 helix: -0.65 (0.39), residues: 170 sheet: -1.53 (0.28), residues: 362 loop : -1.33 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 118 TYR 0.015 0.001 TYR A 507 PHE 0.024 0.002 PHE A 567 TRP 0.011 0.001 TRP C 489 HIS 0.008 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (13658) covalent geometry : angle 0.54285 / 0.29 (18513) SS BOND : bond 0.00218 / 0.13 ( 35) SS BOND : angle 0.75230 / 0.51 ( 70) hydrogen bonds : bond 0.04507 / 3.09 ( 315) hydrogen bonds : angle 6.92177 / 4.70 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.4522 (p90) REVERT: A 342 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8676 (mt) outliers start: 32 outliers final: 22 residues processed: 118 average time/residue: 0.2670 time to fit residues: 45.5767 Evaluate side-chains 111 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 0.0050 chunk 77 optimal weight: 30.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS C 429 HIS C 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.178351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120492 restraints weight = 80803.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.125109 restraints weight = 49085.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.126425 restraints weight = 28991.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.126314 restraints weight = 27405.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.126670 restraints weight = 26491.791| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13693 Z= 0.103 Angle : 0.507 5.533 18583 Z= 0.266 Chirality : 0.043 0.142 1991 Planarity : 0.003 0.046 2396 Dihedral : 4.650 57.309 1814 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 1.95 % Allowed : 16.64 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.77 (0.21), residues: 1630 helix: -0.47 (0.39), residues: 172 sheet: -1.43 (0.28), residues: 366 loop : -1.22 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 383 TYR 0.010 0.001 TYR A 507 PHE 0.018 0.001 PHE B 7 TRP 0.009 0.001 TRP D 28 HIS 0.007 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (13658) covalent geometry : angle 0.50613 / 0.27 (18513) SS BOND : bond 0.00150 / 0.09 ( 35) SS BOND : angle 0.68507 / 0.45 ( 70) hydrogen bonds : bond 0.03610 / 2.46 ( 315) hydrogen bonds : angle 6.50547 / 4.41 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8720 (mt) REVERT: A 387 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6622 (tp) REVERT: A 550 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.6097 (m-70) REVERT: B 38 ARG cc_start: 0.6676 (mmt90) cc_final: 0.6467 (mmt-90) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.2645 time to fit residues: 45.6059 Evaluate side-chains 107 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 70 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 138 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.175125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.117105 restraints weight = 80421.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121477 restraints weight = 48169.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.121191 restraints weight = 28691.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121969 restraints weight = 30437.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.122145 restraints weight = 27443.621| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13693 Z= 0.245 Angle : 0.575 5.570 18583 Z= 0.306 Chirality : 0.045 0.146 1991 Planarity : 0.004 0.047 2396 Dihedral : 4.967 54.683 1814 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.98 % Favored : 88.96 % Rotamer: Outliers : 3.29 % Allowed : 16.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.02 (0.21), residues: 1630 helix: -0.58 (0.39), residues: 172 sheet: -1.62 (0.28), residues: 355 loop : -1.41 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 371 TYR 0.017 0.002 TYR A 507 PHE 0.033 0.002 PHE A 567 TRP 0.015 0.002 TRP C 489 HIS 0.007 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.25 (13658) covalent geometry : angle 0.57447 / 0.31 (18513) SS BOND : bond 0.00286 / 0.16 ( 35) SS BOND : angle 0.77930 / 0.53 ( 70) hydrogen bonds : bond 0.03944 / 2.72 ( 315) hydrogen bonds : angle 6.49876 / 4.43 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.4638 (p90) REVERT: A 57 ILE cc_start: 0.7990 (mt) cc_final: 0.7461 (mt) REVERT: A 70 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4803 (pm20) REVERT: A 342 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8713 (mt) REVERT: A 405 ASN cc_start: 0.8744 (m-40) cc_final: 0.8389 (m-40) REVERT: A 550 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6251 (m-70) REVERT: C 88 PHE cc_start: 0.7850 (t80) cc_final: 0.7643 (t80) REVERT: C 355 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6924 (tt0) outliers start: 49 outliers final: 32 residues processed: 128 average time/residue: 0.2563 time to fit residues: 48.5043 Evaluate side-chains 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 585 SER Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 134 optimal weight: 0.0070 chunk 72 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 41 optimal weight: 0.0980 chunk 129 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.0010 chunk 5 optimal weight: 0.6980 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.178484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.122454 restraints weight = 80750.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125522 restraints weight = 49935.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.125846 restraints weight = 31462.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.126373 restraints weight = 29766.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.126943 restraints weight = 28147.437| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13693 Z= 0.089 Angle : 0.501 5.758 18583 Z= 0.262 Chirality : 0.043 0.149 1991 Planarity : 0.003 0.044 2396 Dihedral : 4.618 57.613 1814 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 2.15 % Allowed : 17.65 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.74 (0.21), residues: 1630 helix: -0.30 (0.39), residues: 172 sheet: -1.49 (0.28), residues: 366 loop : -1.20 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 383 TYR 0.021 0.001 TYR C 401 PHE 0.017 0.001 PHE B 7 TRP 0.011 0.001 TRP D 28 HIS 0.010 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (13658) covalent geometry : angle 0.49976 / 0.26 (18513) SS BOND : bond 0.00134 / 0.08 ( 35) SS BOND : angle 0.68175 / 0.45 ( 70) hydrogen bonds : bond 0.03309 / 2.24 ( 315) hydrogen bonds : angle 6.19155 / 4.21 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.7694 (mt) cc_final: 0.7094 (mt) REVERT: A 70 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.4897 (pm20) REVERT: A 274 CYS cc_start: 0.4565 (OUTLIER) cc_final: 0.3557 (t) REVERT: A 342 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 387 LEU cc_start: 0.6935 (tp) cc_final: 0.6725 (tp) REVERT: A 550 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: C 88 PHE cc_start: 0.7831 (t80) cc_final: 0.7579 (t80) REVERT: C 294 MET cc_start: 0.9079 (tpp) cc_final: 0.8478 (tpp) outliers start: 32 outliers final: 22 residues processed: 126 average time/residue: 0.2533 time to fit residues: 48.2489 Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS C 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.176910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122148 restraints weight = 80986.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124241 restraints weight = 46423.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.123430 restraints weight = 32607.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.124427 restraints weight = 32219.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124608 restraints weight = 29616.992| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13693 Z= 0.160 Angle : 0.528 5.951 18583 Z= 0.276 Chirality : 0.043 0.142 1991 Planarity : 0.003 0.043 2396 Dihedral : 4.713 56.449 1814 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.26 % Favored : 90.67 % Rotamer: Outliers : 2.48 % Allowed : 17.52 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.83 (0.21), residues: 1630 helix: -0.23 (0.40), residues: 172 sheet: -1.59 (0.28), residues: 369 loop : -1.27 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.013 0.001 TYR C 401 PHE 0.022 0.001 PHE A 567 TRP 0.010 0.001 TRP C 489 HIS 0.009 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (13658) covalent geometry : angle 0.52440 / 0.27 (18513) SS BOND : bond 0.00316 / 0.16 ( 35) SS BOND : angle 1.11662 / 0.78 ( 70) hydrogen bonds : bond 0.03381 / 2.30 ( 315) hydrogen bonds : angle 6.11170 / 4.18 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.4684 (p90) REVERT: A 57 ILE cc_start: 0.7802 (mt) cc_final: 0.7233 (mt) REVERT: A 226 VAL cc_start: 0.7555 (p) cc_final: 0.7243 (p) REVERT: A 342 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8682 (mt) REVERT: A 387 LEU cc_start: 0.7100 (tp) cc_final: 0.6865 (tp) REVERT: A 550 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.6151 (m-70) REVERT: C 88 PHE cc_start: 0.7887 (t80) cc_final: 0.7619 (t80) REVERT: C 294 MET cc_start: 0.9087 (tpp) cc_final: 0.8528 (tpp) REVERT: C 355 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6850 (tt0) outliers start: 37 outliers final: 26 residues processed: 119 average time/residue: 0.2543 time to fit residues: 45.2741 Evaluate side-chains 117 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 23 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 156 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.177965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121440 restraints weight = 81002.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.125273 restraints weight = 47038.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125001 restraints weight = 29386.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125749 restraints weight = 30947.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.126050 restraints weight = 27133.296| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13693 Z= 0.109 Angle : 0.502 5.816 18583 Z= 0.262 Chirality : 0.043 0.142 1991 Planarity : 0.003 0.044 2396 Dihedral : 4.607 57.590 1814 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.73 % Favored : 92.21 % Rotamer: Outliers : 2.15 % Allowed : 17.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.74 (0.22), residues: 1630 helix: -0.11 (0.40), residues: 172 sheet: -1.60 (0.27), residues: 375 loop : -1.17 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.014 0.001 TYR C 401 PHE 0.017 0.001 PHE B 7 TRP 0.014 0.001 TRP C 251 HIS 0.009 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13658) covalent geometry : angle 0.49973 / 0.26 (18513) SS BOND : bond 0.00178 / 0.09 ( 35) SS BOND : angle 0.97914 / 0.67 ( 70) hydrogen bonds : bond 0.03163 / 2.15 ( 315) hydrogen bonds : angle 5.94398 / 4.06 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.7827 (mt) cc_final: 0.7252 (mt) REVERT: A 70 GLU cc_start: 0.5625 (OUTLIER) cc_final: 0.4865 (pm20) REVERT: A 342 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8699 (mt) REVERT: A 387 LEU cc_start: 0.7057 (tp) cc_final: 0.6829 (tp) REVERT: A 550 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.6175 (m-70) REVERT: C 88 PHE cc_start: 0.7826 (t80) cc_final: 0.7546 (t80) REVERT: C 294 MET cc_start: 0.9094 (tpp) cc_final: 0.8512 (tpp) outliers start: 32 outliers final: 26 residues processed: 119 average time/residue: 0.2378 time to fit residues: 42.0928 Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.177562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.117475 restraints weight = 81271.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.123483 restraints weight = 44994.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.125623 restraints weight = 29626.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.127023 restraints weight = 21963.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.127478 restraints weight = 20374.979| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13693 Z= 0.129 Angle : 0.508 6.463 18583 Z= 0.265 Chirality : 0.043 0.141 1991 Planarity : 0.003 0.040 2396 Dihedral : 4.609 57.682 1814 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.14 % Favored : 90.80 % Rotamer: Outliers : 2.28 % Allowed : 17.72 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.75 (0.22), residues: 1630 helix: -0.09 (0.40), residues: 172 sheet: -1.60 (0.28), residues: 373 loop : -1.19 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 488 TYR 0.012 0.001 TYR C 401 PHE 0.018 0.001 PHE A 567 TRP 0.013 0.001 TRP C 251 HIS 0.009 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13658) covalent geometry : angle 0.50530 / 0.26 (18513) SS BOND : bond 0.00190 / 0.10 ( 35) SS BOND : angle 0.92974 / 0.64 ( 70) hydrogen bonds : bond 0.03160 / 2.14 ( 315) hydrogen bonds : angle 5.87061 / 4.02 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.7791 (mt) cc_final: 0.7222 (mt) REVERT: A 70 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.4892 (pm20) REVERT: A 342 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8704 (mt) REVERT: A 387 LEU cc_start: 0.7113 (tp) cc_final: 0.6884 (tp) REVERT: A 550 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.6141 (m-70) REVERT: C 88 PHE cc_start: 0.7878 (t80) cc_final: 0.7585 (t80) REVERT: C 294 MET cc_start: 0.9100 (tpp) cc_final: 0.8572 (tpp) REVERT: C 355 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6699 (tt0) outliers start: 34 outliers final: 27 residues processed: 117 average time/residue: 0.2646 time to fit residues: 45.8393 Evaluate side-chains 120 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.177964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.124170 restraints weight = 80861.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.125890 restraints weight = 44872.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.125206 restraints weight = 31865.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.126168 restraints weight = 31940.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.126512 restraints weight = 27979.735| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13693 Z= 0.113 Angle : 0.502 6.755 18583 Z= 0.261 Chirality : 0.043 0.142 1991 Planarity : 0.003 0.043 2396 Dihedral : 4.546 58.397 1814 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 2.15 % Allowed : 17.85 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.68 (0.22), residues: 1630 helix: -0.04 (0.41), residues: 172 sheet: -1.56 (0.28), residues: 373 loop : -1.14 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 383 TYR 0.012 0.001 TYR C 401 PHE 0.016 0.001 PHE B 7 TRP 0.016 0.001 TRP C 251 HIS 0.009 0.001 HIS C 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13658) covalent geometry : angle 0.49972 / 0.26 (18513) SS BOND : bond 0.00171 / 0.09 ( 35) SS BOND : angle 0.88207 / 0.61 ( 70) hydrogen bonds : bond 0.03052 / 2.07 ( 315) hydrogen bonds : angle 5.75865 / 3.94 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.7840 (mt) cc_final: 0.7252 (mt) REVERT: A 70 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.4829 (pm20) REVERT: A 342 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 387 LEU cc_start: 0.7068 (tp) cc_final: 0.6844 (tp) REVERT: A 550 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6227 (m-70) REVERT: C 21 HIS cc_start: 0.8009 (p-80) cc_final: 0.7672 (p-80) REVERT: C 88 PHE cc_start: 0.7629 (t80) cc_final: 0.7352 (t80) REVERT: C 294 MET cc_start: 0.9058 (tpp) cc_final: 0.8516 (tpp) REVERT: C 355 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6801 (tt0) outliers start: 32 outliers final: 28 residues processed: 118 average time/residue: 0.2478 time to fit residues: 42.9987 Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 550 HIS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 788 CYS Chi-restraints excluded: chain C residue 796 ARG Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 810 GLU Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.177973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122059 restraints weight = 80275.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.124147 restraints weight = 50836.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.124590 restraints weight = 32954.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.125701 restraints weight = 29303.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.126076 restraints weight = 26870.537| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 13693 Z= 0.181 Angle : 0.759 57.271 18583 Z= 0.488 Chirality : 0.043 0.141 1991 Planarity : 0.004 0.145 2396 Dihedral : 4.540 58.417 1814 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 2.08 % Allowed : 17.85 % Favored : 80.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.69 (0.22), residues: 1630 helix: -0.04 (0.41), residues: 172 sheet: -1.55 (0.28), residues: 373 loop : -1.15 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.011 0.001 TYR C 401 PHE 0.016 0.001 PHE B 7 TRP 0.013 0.001 TRP C 251 HIS 0.181 0.003 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.18 (13658) covalent geometry : angle 0.75806 / 0.49 (18513) SS BOND : bond 0.00172 / 0.09 ( 35) SS BOND : angle 0.88849 / 0.63 ( 70) hydrogen bonds : bond 0.03046 / 2.07 ( 315) hydrogen bonds : angle 5.75752 / 3.94 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4381.61 seconds wall clock time: 75 minutes 29.33 seconds (4529.33 seconds total)