Starting phenix.real_space_refine on Thu Mar 5 17:03:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl1_25188/03_2026/7sl1_25188_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12534 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 8774 2.51 5 N 2374 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6566 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769} Chain breaks: 5 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6566 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769} Chain breaks: 5 Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 185 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 185 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13830 At special positions: 0 Unit cell: (155.21, 108.73, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2572 8.00 N 2374 7.00 C 8774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.04 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 304 " - pdb=" SG CYS A 308 " 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=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " 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: 1.15 Conformation dependent library (CDL) restraints added in 640.0 milliseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 13.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.195A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.520A pdb=" N ARG A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 4.182A pdb=" N ASN A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.574A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.833A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.183A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.523A pdb=" N ARG B 47 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.217A pdb=" N ASN B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.595A pdb=" N ALA B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.813A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 692 through 711 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.549A pdb=" N CYS E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.563A pdb=" N CYS F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.007A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.007A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU A 62 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.538A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.764A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.764A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N LYS A 369 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 400 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 473 removed outlier: 6.329A pdb=" N GLU A 471 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.797A pdb=" N PHE A 477 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.567A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 607 removed outlier: 3.805A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 765 Processing sheet with id=AB6, first strand: chain 'A' and resid 830 through 832 Processing sheet with id=AB7, first strand: chain 'A' and resid 858 through 864 removed outlier: 3.790A pdb=" N LEU A 846 " --> pdb=" O THR A 891 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 848 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 889 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 905 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 7 through 14 removed outlier: 7.010A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 12 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 36 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 14 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET B 38 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 7 through 14 removed outlier: 7.010A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 12 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 36 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 14 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET B 38 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LEU B 62 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.537A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.925A pdb=" N CYS B 312 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.176A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS B 425 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 400 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.329A pdb=" N GLU B 471 " --> pdb=" O LYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.612A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.586A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 604 through 607 removed outlier: 3.636A pdb=" N ILE B 613 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 765 Processing sheet with id=AD4, first strand: chain 'B' and resid 830 through 832 Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 864 removed outlier: 3.787A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 848 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 889 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 905 " --> pdb=" O TYR B 884 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4533 1.35 - 1.47: 3389 1.47 - 1.59: 6108 1.59 - 1.71: 0 1.71 - 1.83: 134 Bond restraints: 14164 Sorted by residual: bond pdb=" N ASP B 234 " pdb=" CA ASP B 234 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CA GLN B 538 " pdb=" CB GLN B 538 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.28e+00 bond pdb=" N TYR A 144 " pdb=" CA TYR A 144 " ideal model delta sigma weight residual 1.465 1.451 0.014 1.31e-02 5.83e+03 1.13e+00 bond pdb=" CA ASP B 464 " pdb=" C ASP B 464 " ideal model delta sigma weight residual 1.520 1.515 0.005 4.80e-03 4.34e+04 9.56e-01 bond pdb=" CG GLU B 391 " pdb=" CD GLU B 391 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.78e-01 ... (remaining 14159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 18839 2.01 - 4.02: 310 4.02 - 6.02: 29 6.02 - 8.03: 6 8.03 - 10.04: 2 Bond angle restraints: 19186 Sorted by residual: angle pdb=" C THR A 167 " pdb=" N ASN A 168 " pdb=" CA ASN A 168 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C THR B 167 " pdb=" N ASN B 168 " pdb=" CA ASN B 168 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG A 454 " pdb=" N ASN A 455 " pdb=" CA ASN A 455 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 angle pdb=" C ARG B 454 " pdb=" N ASN B 455 " pdb=" CA ASN B 455 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" C PRO B 837 " pdb=" N LYS B 838 " pdb=" CA LYS B 838 " ideal model delta sigma weight residual 120.38 124.71 -4.33 1.46e+00 4.69e-01 8.82e+00 ... (remaining 19181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7633 17.12 - 34.25: 782 34.25 - 51.37: 156 51.37 - 68.49: 23 68.49 - 85.61: 8 Dihedral angle restraints: 8602 sinusoidal: 3600 harmonic: 5002 Sorted by residual: dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -159.08 73.08 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 188 " pdb=" CB CYS B 188 " ideal model delta sinusoidal sigma weight residual -86.00 -158.95 72.95 1 1.00e+01 1.00e-02 6.79e+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 93.00 163.28 -70.28 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1198 0.028 - 0.056: 506 0.056 - 0.083: 191 0.083 - 0.111: 128 0.111 - 0.139: 53 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 341 " pdb=" N ILE A 341 " pdb=" C ILE A 341 " pdb=" CB ILE A 341 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 341 " pdb=" N ILE B 341 " pdb=" C ILE B 341 " pdb=" CB ILE B 341 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2073 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 169 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 170 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 169 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO B 170 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 16 " -0.009 2.00e-02 2.50e+03 1.23e-02 3.00e+00 pdb=" CG TYR C 16 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 16 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 16 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 16 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 16 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 16 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 16 " 0.000 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 677 2.73 - 3.27: 13737 3.27 - 3.81: 22587 3.81 - 4.36: 28015 4.36 - 4.90: 46799 Nonbonded interactions: 111815 Sorted by model distance: nonbonded pdb=" OD1 ASN B 295 " pdb=" OG SER B 297 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLN A 406 " pdb=" NE2 GLN B 406 " model vdw 2.188 3.120 nonbonded pdb=" OD1 ASN A 295 " pdb=" OG SER A 297 " model vdw 2.192 3.040 nonbonded pdb=" OG SER A 399 " pdb=" O GLN A 423 " model vdw 2.195 3.040 nonbonded pdb=" OG SER B 399 " pdb=" O GLN B 423 " model vdw 2.200 3.040 ... (remaining 111810 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.002 0.045 14206 Z= 0.108 Angle : 0.599 10.038 19270 Z= 0.317 Chirality : 0.044 0.139 2076 Planarity : 0.003 0.048 2480 Dihedral : 13.617 85.613 5248 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.79 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1682 helix: 0.30 (0.41), residues: 180 sheet: -0.83 (0.27), residues: 384 loop : -0.80 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.030 0.001 TYR C 16 PHE 0.011 0.001 PHE A 178 TRP 0.009 0.001 TRP A 834 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00232 (14164) covalent geometry : angle 0.59670 (19186) SS BOND : bond 0.00210 ( 42) SS BOND : angle 1.05348 ( 84) hydrogen bonds : bond 0.25490 ( 317) hydrogen bonds : angle 9.04431 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8262 (mmt) cc_final: 0.8057 (mmp) REVERT: A 863 VAL cc_start: 0.8018 (t) cc_final: 0.7709 (t) REVERT: B 794 ASP cc_start: 0.7362 (t70) cc_final: 0.7081 (t70) REVERT: B 863 VAL cc_start: 0.8082 (t) cc_final: 0.7769 (t) REVERT: D 22 ARG cc_start: 0.6801 (ptt90) cc_final: 0.6585 (ptt90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1320 time to fit residues: 22.2991 Evaluate side-chains 84 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 455 ASN ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063688 restraints weight = 41701.921| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.67 r_work: 0.3046 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 14206 Z= 0.256 Angle : 0.678 10.442 19270 Z= 0.351 Chirality : 0.047 0.155 2076 Planarity : 0.004 0.049 2480 Dihedral : 5.075 24.342 1870 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.71 % Allowed : 7.46 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1682 helix: 0.25 (0.39), residues: 182 sheet: -0.73 (0.26), residues: 410 loop : -0.98 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 872 TYR 0.024 0.002 TYR B 633 PHE 0.019 0.002 PHE A 178 TRP 0.007 0.001 TRP A 529 HIS 0.010 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00600 (14164) covalent geometry : angle 0.67192 (19186) SS BOND : bond 0.00382 ( 42) SS BOND : angle 1.50758 ( 84) hydrogen bonds : bond 0.05964 ( 317) hydrogen bonds : angle 7.07850 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7196 (ptt90) REVERT: B 318 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7687 (mp0) REVERT: B 454 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.7137 (ptt90) REVERT: B 794 ASP cc_start: 0.7855 (t70) cc_final: 0.7493 (t70) REVERT: E 18 ASN cc_start: 0.8806 (m110) cc_final: 0.8603 (m110) REVERT: F 14 TYR cc_start: 0.7857 (m-80) cc_final: 0.7529 (m-80) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.1277 time to fit residues: 20.1704 Evaluate side-chains 93 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 17 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 161 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.088677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064723 restraints weight = 42249.265| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.66 r_work: 0.3081 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14206 Z= 0.162 Angle : 0.611 11.026 19270 Z= 0.314 Chirality : 0.045 0.151 2076 Planarity : 0.004 0.047 2480 Dihedral : 4.983 21.867 1870 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.71 % Allowed : 10.03 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.21), residues: 1682 helix: 0.35 (0.39), residues: 182 sheet: -0.78 (0.26), residues: 406 loop : -0.99 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 479 TYR 0.018 0.001 TYR B 507 PHE 0.019 0.001 PHE B 703 TRP 0.006 0.001 TRP B 529 HIS 0.005 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00381 (14164) covalent geometry : angle 0.60725 (19186) SS BOND : bond 0.00230 ( 42) SS BOND : angle 1.18646 ( 84) hydrogen bonds : bond 0.04387 ( 317) hydrogen bonds : angle 6.56052 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.9054 (mmt) cc_final: 0.8843 (mmt) REVERT: A 454 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7120 (ptt90) REVERT: A 901 GLU cc_start: 0.8040 (pp20) cc_final: 0.7751 (pp20) REVERT: B 318 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7595 (mp0) REVERT: B 454 ARG cc_start: 0.7784 (tpt-90) cc_final: 0.7108 (ptt90) REVERT: B 794 ASP cc_start: 0.7810 (t70) cc_final: 0.7433 (t70) REVERT: D 22 ARG cc_start: 0.7074 (ptt90) cc_final: 0.6695 (ptt90) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.1250 time to fit residues: 18.8522 Evaluate side-chains 88 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 21 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 166 optimal weight: 0.0050 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 153 optimal weight: 0.0170 chunk 108 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.090008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066573 restraints weight = 42915.999| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.65 r_work: 0.3135 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14206 Z= 0.107 Angle : 0.577 11.371 19270 Z= 0.293 Chirality : 0.044 0.149 2076 Planarity : 0.003 0.045 2480 Dihedral : 4.776 20.355 1870 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.84 % Allowed : 11.31 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.21), residues: 1682 helix: 0.63 (0.39), residues: 182 sheet: -0.64 (0.26), residues: 396 loop : -0.98 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.017 0.001 TYR B 507 PHE 0.019 0.001 PHE B 703 TRP 0.007 0.001 TRP B 834 HIS 0.003 0.001 HIS B 831 Details of bonding type rmsd covalent geometry : bond 0.00251 (14164) covalent geometry : angle 0.57451 (19186) SS BOND : bond 0.00220 ( 42) SS BOND : angle 1.00786 ( 84) hydrogen bonds : bond 0.03862 ( 317) hydrogen bonds : angle 6.19915 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 454 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.7110 (ptt90) REVERT: B 454 ARG cc_start: 0.7789 (tpt-90) cc_final: 0.7100 (ptt90) REVERT: B 794 ASP cc_start: 0.7713 (t70) cc_final: 0.7320 (t70) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.1113 time to fit residues: 16.7481 Evaluate side-chains 89 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 125 optimal weight: 0.0170 chunk 47 optimal weight: 4.9990 chunk 111 optimal weight: 0.0070 chunk 133 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 0.0020 overall best weight: 1.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066594 restraints weight = 42139.473| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.52 r_work: 0.3136 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14206 Z= 0.123 Angle : 0.581 11.891 19270 Z= 0.294 Chirality : 0.045 0.169 2076 Planarity : 0.003 0.046 2480 Dihedral : 4.756 20.339 1870 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.96 % Allowed : 12.53 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1682 helix: 0.78 (0.40), residues: 180 sheet: -0.60 (0.26), residues: 396 loop : -0.96 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.022 0.001 TYR E 19 PHE 0.019 0.001 PHE B 703 TRP 0.007 0.001 TRP B 553 HIS 0.002 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00292 (14164) covalent geometry : angle 0.57848 (19186) SS BOND : bond 0.00227 ( 42) SS BOND : angle 1.01996 ( 84) hydrogen bonds : bond 0.03655 ( 317) hydrogen bonds : angle 5.93240 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8580 (tpt) cc_final: 0.8320 (tpt) REVERT: A 454 ARG cc_start: 0.7796 (tpt-90) cc_final: 0.7125 (ptt90) REVERT: A 901 GLU cc_start: 0.7951 (pp20) cc_final: 0.7607 (pp20) REVERT: B 56 MET cc_start: 0.8587 (tpt) cc_final: 0.8329 (tpt) REVERT: B 454 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7125 (ptt90) REVERT: B 794 ASP cc_start: 0.7748 (t70) cc_final: 0.7354 (t70) REVERT: E 5 GLN cc_start: 0.8159 (tt0) cc_final: 0.7935 (tt0) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.1046 time to fit residues: 16.5891 Evaluate side-chains 92 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 57 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN E 5 GLN E 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.088685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066218 restraints weight = 41618.541| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.43 r_work: 0.3118 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14206 Z= 0.177 Angle : 0.602 13.310 19270 Z= 0.305 Chirality : 0.045 0.163 2076 Planarity : 0.004 0.046 2480 Dihedral : 4.865 20.488 1870 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.96 % Allowed : 13.50 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1682 helix: 0.85 (0.41), residues: 178 sheet: -0.73 (0.26), residues: 406 loop : -0.96 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 556 TYR 0.023 0.001 TYR E 19 PHE 0.019 0.001 PHE B 703 TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00420 (14164) covalent geometry : angle 0.59847 (19186) SS BOND : bond 0.00237 ( 42) SS BOND : angle 1.13816 ( 84) hydrogen bonds : bond 0.03680 ( 317) hydrogen bonds : angle 5.87372 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 ARG cc_start: 0.7795 (tpt-90) cc_final: 0.7176 (ptt90) REVERT: B 454 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7162 (ptt90) REVERT: B 794 ASP cc_start: 0.7751 (t70) cc_final: 0.7352 (t70) REVERT: E 12 SER cc_start: 0.8521 (t) cc_final: 0.8120 (p) outliers start: 15 outliers final: 14 residues processed: 95 average time/residue: 0.0997 time to fit residues: 15.2030 Evaluate side-chains 94 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066323 restraints weight = 42313.927| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.61 r_work: 0.3128 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14206 Z= 0.119 Angle : 0.577 13.043 19270 Z= 0.292 Chirality : 0.044 0.173 2076 Planarity : 0.003 0.042 2480 Dihedral : 4.766 20.213 1870 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.03 % Allowed : 13.69 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.21), residues: 1682 helix: 0.92 (0.41), residues: 178 sheet: -0.62 (0.26), residues: 396 loop : -1.00 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.018 0.001 TYR E 19 PHE 0.019 0.001 PHE B 703 TRP 0.009 0.001 TRP B 834 HIS 0.002 0.000 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00285 (14164) covalent geometry : angle 0.57502 (19186) SS BOND : bond 0.00204 ( 42) SS BOND : angle 0.98970 ( 84) hydrogen bonds : bond 0.03473 ( 317) hydrogen bonds : angle 5.71618 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8580 (tpt) cc_final: 0.8295 (tpt) REVERT: A 454 ARG cc_start: 0.7772 (tpt-90) cc_final: 0.7150 (ptt90) REVERT: A 893 LEU cc_start: 0.9524 (mt) cc_final: 0.9290 (mp) REVERT: B 454 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7185 (ptt90) REVERT: B 794 ASP cc_start: 0.7741 (t70) cc_final: 0.7335 (t70) REVERT: B 893 LEU cc_start: 0.9513 (mt) cc_final: 0.9267 (mp) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.1015 time to fit residues: 16.5308 Evaluate side-chains 95 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 155 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 0.0000 chunk 142 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 144 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN B 349 ASN F 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.090193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.066796 restraints weight = 42519.645| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.62 r_work: 0.3143 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14206 Z= 0.102 Angle : 0.574 12.928 19270 Z= 0.289 Chirality : 0.044 0.198 2076 Planarity : 0.003 0.043 2480 Dihedral : 4.649 19.637 1870 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.41 % Allowed : 14.01 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1682 helix: 0.88 (0.40), residues: 180 sheet: -0.57 (0.26), residues: 396 loop : -0.98 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 556 TYR 0.021 0.001 TYR D 16 PHE 0.019 0.001 PHE B 703 TRP 0.012 0.001 TRP B 834 HIS 0.002 0.000 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00242 (14164) covalent geometry : angle 0.57161 (19186) SS BOND : bond 0.00217 ( 42) SS BOND : angle 0.94497 ( 84) hydrogen bonds : bond 0.03368 ( 317) hydrogen bonds : angle 5.60285 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8535 (tpt) cc_final: 0.8221 (tpt) REVERT: A 454 ARG cc_start: 0.7768 (tpt-90) cc_final: 0.7126 (ptt90) REVERT: A 893 LEU cc_start: 0.9476 (mt) cc_final: 0.9256 (mp) REVERT: B 454 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.7154 (ptt90) REVERT: B 794 ASP cc_start: 0.7747 (t70) cc_final: 0.7334 (t70) REVERT: B 893 LEU cc_start: 0.9476 (mt) cc_final: 0.9232 (mp) REVERT: E 14 TYR cc_start: 0.8009 (m-80) cc_final: 0.7726 (m-80) REVERT: F 12 SER cc_start: 0.8341 (t) cc_final: 0.7877 (p) REVERT: F 14 TYR cc_start: 0.7819 (m-80) cc_final: 0.7468 (m-80) outliers start: 22 outliers final: 19 residues processed: 103 average time/residue: 0.0902 time to fit residues: 15.0544 Evaluate side-chains 99 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 162 optimal weight: 0.0270 chunk 158 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.089912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065974 restraints weight = 43272.138| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.70 r_work: 0.3115 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14206 Z= 0.106 Angle : 0.599 13.590 19270 Z= 0.300 Chirality : 0.045 0.229 2076 Planarity : 0.003 0.053 2480 Dihedral : 4.632 19.496 1870 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.22 % Allowed : 14.52 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1682 helix: 0.66 (0.39), residues: 192 sheet: -0.53 (0.27), residues: 396 loop : -1.01 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.037 0.001 TYR F 19 PHE 0.019 0.001 PHE B 703 TRP 0.011 0.001 TRP B 834 HIS 0.002 0.000 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00258 (14164) covalent geometry : angle 0.59192 (19186) SS BOND : bond 0.00221 ( 42) SS BOND : angle 1.50008 ( 84) hydrogen bonds : bond 0.03366 ( 317) hydrogen bonds : angle 5.57730 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.8545 (tpt) cc_final: 0.8247 (tpt) REVERT: A 454 ARG cc_start: 0.7786 (tpt-90) cc_final: 0.7105 (ptt90) REVERT: A 893 LEU cc_start: 0.9463 (mt) cc_final: 0.9236 (mp) REVERT: B 454 ARG cc_start: 0.7842 (tpt-90) cc_final: 0.7141 (ptt90) REVERT: B 794 ASP cc_start: 0.7789 (t70) cc_final: 0.7374 (t70) REVERT: B 893 LEU cc_start: 0.9458 (mt) cc_final: 0.9213 (mp) REVERT: E 14 TYR cc_start: 0.7977 (m-80) cc_final: 0.7707 (m-80) REVERT: F 12 SER cc_start: 0.8311 (t) cc_final: 0.7812 (p) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 0.0998 time to fit residues: 15.2312 Evaluate side-chains 93 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065332 restraints weight = 43064.623| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.68 r_work: 0.3102 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14206 Z= 0.124 Angle : 0.600 14.395 19270 Z= 0.301 Chirality : 0.045 0.166 2076 Planarity : 0.003 0.058 2480 Dihedral : 4.687 19.556 1870 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.09 % Allowed : 14.52 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1682 helix: 0.90 (0.41), residues: 180 sheet: -0.63 (0.26), residues: 406 loop : -0.92 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.035 0.001 TYR F 19 PHE 0.018 0.001 PHE B 703 TRP 0.009 0.001 TRP A 834 HIS 0.002 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00300 (14164) covalent geometry : angle 0.59488 (19186) SS BOND : bond 0.00226 ( 42) SS BOND : angle 1.32539 ( 84) hydrogen bonds : bond 0.03357 ( 317) hydrogen bonds : angle 5.56909 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 454 ARG cc_start: 0.7834 (tpt-90) cc_final: 0.7148 (ptt90) REVERT: B 454 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7186 (ptt90) REVERT: B 794 ASP cc_start: 0.7811 (t70) cc_final: 0.7386 (t70) REVERT: B 893 LEU cc_start: 0.9455 (mt) cc_final: 0.9216 (mp) outliers start: 17 outliers final: 16 residues processed: 92 average time/residue: 0.1005 time to fit residues: 14.9432 Evaluate side-chains 93 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 162 optimal weight: 0.0980 chunk 151 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.088978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065495 restraints weight = 42884.625| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.59 r_work: 0.3113 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14206 Z= 0.151 Angle : 0.605 13.795 19270 Z= 0.304 Chirality : 0.045 0.169 2076 Planarity : 0.004 0.059 2480 Dihedral : 4.737 19.845 1870 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.41 % Allowed : 14.33 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1682 helix: 0.94 (0.41), residues: 180 sheet: -0.65 (0.26), residues: 406 loop : -0.91 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 479 TYR 0.027 0.001 TYR F 19 PHE 0.018 0.001 PHE B 703 TRP 0.007 0.001 TRP B 553 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00363 (14164) covalent geometry : angle 0.60005 (19186) SS BOND : bond 0.00201 ( 42) SS BOND : angle 1.33251 ( 84) hydrogen bonds : bond 0.03395 ( 317) hydrogen bonds : angle 5.56785 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.88 seconds wall clock time: 54 minutes 11.23 seconds (3251.23 seconds total)