Starting phenix.real_space_refine on Fri Jul 3 16:36:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.map" model { file = "/net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znz_60281/07_2026/8znz_60281.cif" } resolution = 3.06 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= 0.023 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 S 70 5.16 5 Na 2 4.78 5 C 9618 2.51 5 N 2566 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 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: 15154 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4089 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 796 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 1, ' CA': 1} Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Restraints were copied for chains: B, C, D, G, H Time building chain proxies: 4.51, per 1000 atoms: 0.30 Number of scatterers: 15154 At special positions: 0 Unit cell: (148.05, 126.054, 115.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 70 16.00 Na 2 11.00 O 2892 8.00 N 2566 7.00 C 9618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 57 " distance=2.02 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 358 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 387 " distance=2.07 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 479 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.08 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.06 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 57 " distance=2.02 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 358 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 387 " distance=2.07 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 479 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.08 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.06 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: 1.20 Conformation dependent library (CDL) restraints added in 654.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 220 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 243 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 38 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 220 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 243 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 38 " 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 32 sheets defined 19.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.664A pdb=" N LEU A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.628A pdb=" N VAL A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 123 through 129 removed outlier: 4.070A pdb=" N GLU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.835A pdb=" N LYS A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.953A pdb=" N GLN A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.530A pdb=" N ALA A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.988A pdb=" N ASP A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.592A pdb=" N ASP A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.638A pdb=" N ASN A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.674A pdb=" N GLY A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.901A pdb=" N LYS A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.832A pdb=" N LYS F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.654A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.546A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.664A pdb=" N LEU B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.628A pdb=" N VAL B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 123 through 129 removed outlier: 4.070A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.835A pdb=" N LYS B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.953A pdb=" N GLN B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.530A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.988A pdb=" N ASP B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.592A pdb=" N ASP B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.638A pdb=" N ASN B 362 " --> pdb=" O CYS B 358 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 504 through 507 removed outlier: 3.674A pdb=" N GLY B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 508 through 514 removed outlier: 3.901A pdb=" N LYS B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.832A pdb=" N LYS D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.654A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.546A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU A 29 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 302 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 8.662A pdb=" N ILE A 216 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 172 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU A 218 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS A 220 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 176 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 215 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL A 240 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 239 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 275 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 267 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 390 Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 486 removed outlier: 4.123A pdb=" N LYS A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 547 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 18 through 24 removed outlier: 3.519A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.534A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.516A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.966A pdb=" N MET F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 59 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.691A pdb=" N SER I 25 " --> pdb=" O VAL I 2 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER I 57 " --> pdb=" O HIS I 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS I 52 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER I 57 " --> pdb=" O HIS I 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS I 52 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR I 94 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 5 through 6 removed outlier: 6.500A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.529A pdb=" N TYR J 49 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 34 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 89 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU B 29 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 302 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AC1, first strand: chain 'B' and resid 161 through 166 removed outlier: 8.662A pdb=" N ILE B 216 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 172 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 218 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 174 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS B 220 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR B 176 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 215 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL B 240 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA B 217 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 239 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 275 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 267 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC3, first strand: chain 'B' and resid 387 through 390 Processing sheet with id=AC4, first strand: chain 'B' and resid 493 through 498 Processing sheet with id=AC5, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.123A pdb=" N LYS B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 547 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 18 through 24 removed outlier: 3.519A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.534A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.516A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.966A pdb=" N MET D 34 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 59 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 2 through 3 removed outlier: 3.691A pdb=" N SER G 25 " --> pdb=" O VAL G 2 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER G 57 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS G 52 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER G 57 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS G 52 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 6 removed outlier: 6.500A pdb=" N THR H 69 " --> pdb=" O ALA H 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.529A pdb=" N TYR H 49 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 34 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 89 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1152 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: 2.56 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3018 1.33 - 1.45: 4646 1.45 - 1.58: 7730 1.58 - 1.71: 0 1.71 - 1.84: 108 Bond restraints: 15502 Sorted by residual: bond pdb=" CA LYS G 74 " pdb=" C LYS G 74 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" CA LYS I 74 " pdb=" C LYS I 74 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" N TYR H 94 " pdb=" CA TYR H 94 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" N TYR J 94 " pdb=" CA TYR J 94 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta sigma weight residual 1.527 1.472 0.054 1.44e-02 4.82e+03 1.43e+01 ... (remaining 15497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 20452 2.78 - 5.55: 506 5.55 - 8.33: 50 8.33 - 11.11: 8 11.11 - 13.88: 4 Bond angle restraints: 21020 Sorted by residual: angle pdb=" N CYS B 57 " pdb=" CA CYS B 57 " pdb=" C CYS B 57 " ideal model delta sigma weight residual 108.74 97.93 10.81 1.38e+00 5.25e-01 6.14e+01 angle pdb=" N CYS A 57 " pdb=" CA CYS A 57 " pdb=" C CYS A 57 " ideal model delta sigma weight residual 108.74 97.93 10.81 1.38e+00 5.25e-01 6.14e+01 angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 113.40 123.61 -10.21 1.47e+00 4.63e-01 4.82e+01 angle pdb=" N LYS B 97 " pdb=" CA LYS B 97 " pdb=" C LYS B 97 " ideal model delta sigma weight residual 113.40 123.61 -10.21 1.47e+00 4.63e-01 4.82e+01 angle pdb=" CA THR C 5 " pdb=" C THR C 5 " pdb=" O THR C 5 " ideal model delta sigma weight residual 120.81 112.87 7.94 1.15e+00 7.56e-01 4.77e+01 ... (remaining 21015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8034 17.89 - 35.79: 888 35.79 - 53.68: 196 53.68 - 71.58: 44 71.58 - 89.47: 20 Dihedral angle restraints: 9182 sinusoidal: 3608 harmonic: 5574 Sorted by residual: dihedral pdb=" CD ARG A 56 " pdb=" NE ARG A 56 " pdb=" CZ ARG A 56 " pdb=" NH1 ARG A 56 " ideal model delta sinusoidal sigma weight residual 0.00 -87.76 87.76 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG B 56 " pdb=" NE ARG B 56 " pdb=" CZ ARG B 56 " pdb=" NH1 ARG B 56 " ideal model delta sinusoidal sigma weight residual 0.00 -87.76 87.76 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG A 297 " pdb=" NE ARG A 297 " pdb=" CZ ARG A 297 " pdb=" NH1 ARG A 297 " ideal model delta sinusoidal sigma weight residual 0.00 -80.69 80.69 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 9179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2142 0.127 - 0.254: 120 0.254 - 0.380: 20 0.380 - 0.507: 0 0.507 - 0.634: 6 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA LYS A 97 " pdb=" N LYS A 97 " pdb=" C LYS A 97 " pdb=" CB LYS A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA LYS B 97 " pdb=" N LYS B 97 " pdb=" C LYS B 97 " pdb=" CB LYS B 97 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA THR B 90 " pdb=" N THR B 90 " pdb=" C THR B 90 " pdb=" CB THR B 90 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.49e+00 ... (remaining 2285 not shown) Planarity restraints: 2698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 56 " 1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 56 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 56 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 56 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 56 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 56 " 1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 56 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 56 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 56 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 56 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 297 " -1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A 297 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 297 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 297 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 297 " -0.019 2.00e-02 2.50e+03 ... (remaining 2695 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 254 2.63 - 3.20: 13208 3.20 - 3.76: 20476 3.76 - 4.33: 30880 4.33 - 4.90: 53331 Nonbonded interactions: 118149 Sorted by model distance: nonbonded pdb=" OD1 ASP G 109 " pdb=" N VAL G 110 " model vdw 2.059 3.120 nonbonded pdb=" OD1 ASP I 109 " pdb=" N VAL I 110 " model vdw 2.059 3.120 nonbonded pdb=" O ASN I 54 " pdb=" OG SER I 55 " model vdw 2.062 3.040 nonbonded pdb=" O ASN G 54 " pdb=" OG SER G 55 " model vdw 2.062 3.040 nonbonded pdb=" OD2 ASP B 85 " pdb="ZN ZN B 601 " model vdw 2.068 2.230 ... (remaining 118144 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'H' } 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 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: 8.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.374 15524 Z= 0.490 Angle : 1.039 13.882 21052 Z= 0.660 Chirality : 0.077 0.634 2288 Planarity : 0.027 0.494 2698 Dihedral : 16.228 89.470 5602 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.97 % Allowed : 4.74 % Favored : 94.28 % Cbeta Deviations : 0.34 % 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: -3.29 (0.17), residues: 1924 helix: -1.62 (0.28), residues: 266 sheet: -1.49 (0.22), residues: 586 loop : -2.84 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 401 TYR 0.047 0.005 TYR J 94 PHE 0.020 0.004 PHE A 183 TRP 0.024 0.003 TRP D 47 HIS 0.007 0.002 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.45 (15502) covalent geometry : angle 1.03440 / 0.66 (21020) SS BOND : bond 0.02384 / 1.42 ( 16) SS BOND : angle 2.58834 / 1.89 ( 32) hydrogen bonds : bond 0.23461 / 15.51 ( 410) hydrogen bonds : angle 9.18213 / 6.45 ( 1152) metal coordination : bond 0.27287 / 15.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.516 Fit side-chains REVERT: A 87 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: J 94 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.5592 (t80) REVERT: B 87 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: H 94 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5594 (t80) outliers start: 16 outliers final: 0 residues processed: 236 average time/residue: 0.1318 time to fit residues: 45.6555 Evaluate side-chains 210 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 88 GLN I 52 HIS J 79 GLN B 69 GLN B 88 GLN G 52 HIS H 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117522 restraints weight = 19655.437| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.39 r_work: 0.3324 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15524 Z= 0.137 Angle : 0.695 11.955 21052 Z= 0.363 Chirality : 0.049 0.234 2288 Planarity : 0.005 0.091 2698 Dihedral : 5.696 54.958 2130 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.70 % Allowed : 9.98 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.11 % 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: -2.41 (0.18), residues: 1924 helix: -0.46 (0.29), residues: 288 sheet: -0.86 (0.22), residues: 590 loop : -2.46 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 87 TYR 0.020 0.001 TYR I 99 PHE 0.019 0.001 PHE J 71 TRP 0.011 0.001 TRP F 47 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15502) covalent geometry : angle 0.68559 / 0.36 (21020) SS BOND : bond 0.00394 / 0.23 ( 16) SS BOND : angle 2.93208 / 2.16 ( 32) hydrogen bonds : bond 0.04369 / 2.97 ( 410) hydrogen bonds : angle 5.85565 / 4.13 ( 1152) metal coordination : bond 0.00664 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.7832 (mttm) cc_final: 0.7458 (mtpp) REVERT: I 105 GLU cc_start: 0.7711 (mp0) cc_final: 0.7376 (mp0) REVERT: J 20 THR cc_start: 0.6815 (p) cc_final: 0.6322 (m) REVERT: B 330 LYS cc_start: 0.7829 (mttm) cc_final: 0.7457 (mtpp) REVERT: G 105 GLU cc_start: 0.7703 (mp0) cc_final: 0.7362 (mp0) REVERT: H 20 THR cc_start: 0.6839 (p) cc_final: 0.6346 (m) outliers start: 28 outliers final: 22 residues processed: 236 average time/residue: 0.1252 time to fit residues: 43.7973 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115217 restraints weight = 20149.218| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.47 r_work: 0.3283 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15524 Z= 0.128 Angle : 0.617 7.858 21052 Z= 0.324 Chirality : 0.048 0.205 2288 Planarity : 0.005 0.091 2698 Dihedral : 5.523 57.232 2130 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.22 % Allowed : 14.23 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.99 (0.19), residues: 1924 helix: -0.27 (0.29), residues: 298 sheet: -0.53 (0.23), residues: 568 loop : -2.16 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 87 TYR 0.019 0.001 TYR C 91 PHE 0.021 0.001 PHE B 380 TRP 0.012 0.001 TRP F 47 HIS 0.004 0.001 HIS H 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15502) covalent geometry : angle 0.61235 / 0.32 (21020) SS BOND : bond 0.00433 / 0.25 ( 16) SS BOND : angle 2.09124 / 1.51 ( 32) hydrogen bonds : bond 0.04000 / 2.73 ( 410) hydrogen bonds : angle 5.24485 / 3.70 ( 1152) metal coordination : bond 0.00402 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.635 Fit side-chains REVERT: A 129 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 134 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7275 (mp0) REVERT: A 330 LYS cc_start: 0.7891 (mttm) cc_final: 0.7569 (mtpp) REVERT: A 379 MET cc_start: 0.8491 (tmm) cc_final: 0.8125 (tmm) REVERT: I 105 GLU cc_start: 0.7709 (mp0) cc_final: 0.7445 (mp0) REVERT: J 20 THR cc_start: 0.6915 (p) cc_final: 0.6423 (m) REVERT: J 54 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7981 (ttm110) REVERT: J 90 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7534 (pp30) REVERT: J 94 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.6108 (t80) REVERT: B 129 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 134 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7260 (mp0) REVERT: B 330 LYS cc_start: 0.7890 (mttm) cc_final: 0.7569 (mtpp) REVERT: B 379 MET cc_start: 0.8469 (tmm) cc_final: 0.8099 (tmm) REVERT: G 105 GLU cc_start: 0.7700 (mp0) cc_final: 0.7427 (mp0) REVERT: H 20 THR cc_start: 0.6935 (p) cc_final: 0.6443 (m) REVERT: H 54 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7978 (ttm110) REVERT: H 90 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7531 (pp30) REVERT: H 94 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.6102 (t80) outliers start: 20 outliers final: 14 residues processed: 216 average time/residue: 0.1279 time to fit residues: 40.6549 Evaluate side-chains 214 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 0.0570 chunk 2 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114586 restraints weight = 20155.058| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.42 r_work: 0.3287 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15524 Z= 0.117 Angle : 0.587 7.103 21052 Z= 0.307 Chirality : 0.046 0.180 2288 Planarity : 0.005 0.091 2698 Dihedral : 5.402 57.047 2130 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.01 % Allowed : 15.02 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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 (0.19), residues: 1924 helix: 0.15 (0.31), residues: 294 sheet: -0.39 (0.23), residues: 568 loop : -2.05 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.019 0.001 TYR E 91 PHE 0.021 0.001 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15502) covalent geometry : angle 0.58207 / 0.31 (21020) SS BOND : bond 0.00379 / 0.22 ( 16) SS BOND : angle 2.06115 / 1.49 ( 32) hydrogen bonds : bond 0.03653 / 2.51 ( 410) hydrogen bonds : angle 4.89814 / 3.46 ( 1152) metal coordination : bond 0.00203 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.592 Fit side-chains REVERT: A 129 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 134 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7266 (mp0) REVERT: A 330 LYS cc_start: 0.7857 (mttm) cc_final: 0.7513 (mtpp) REVERT: A 402 ASN cc_start: 0.8324 (t0) cc_final: 0.8096 (t0) REVERT: I 20 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7226 (mt) REVERT: I 30 THR cc_start: 0.8548 (m) cc_final: 0.8347 (t) REVERT: J 20 THR cc_start: 0.6893 (p) cc_final: 0.6625 (m) REVERT: J 54 ARG cc_start: 0.8235 (ttm110) cc_final: 0.8019 (ttm110) REVERT: J 90 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7676 (pp30) REVERT: J 94 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 129 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 134 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7243 (mp0) REVERT: B 330 LYS cc_start: 0.7863 (mttm) cc_final: 0.7522 (mtpp) REVERT: G 20 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7222 (mt) REVERT: G 30 THR cc_start: 0.8558 (m) cc_final: 0.8357 (t) REVERT: H 20 THR cc_start: 0.6905 (p) cc_final: 0.6637 (m) REVERT: H 54 ARG cc_start: 0.8233 (ttm110) cc_final: 0.8022 (ttm110) REVERT: H 90 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7681 (pp30) REVERT: H 94 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6286 (t80) outliers start: 33 outliers final: 26 residues processed: 221 average time/residue: 0.1139 time to fit residues: 37.9237 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109954 restraints weight = 20245.897| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.47 r_work: 0.3215 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15524 Z= 0.180 Angle : 0.657 8.004 21052 Z= 0.342 Chirality : 0.049 0.220 2288 Planarity : 0.005 0.088 2698 Dihedral : 5.703 55.554 2130 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.92 % Allowed : 16.55 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.81 (0.19), residues: 1924 helix: -0.08 (0.30), residues: 294 sheet: -0.38 (0.23), residues: 594 loop : -2.10 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.027 0.002 TYR C 94 PHE 0.019 0.002 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.006 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (15502) covalent geometry : angle 0.65078 / 0.34 (21020) SS BOND : bond 0.00512 / 0.29 ( 16) SS BOND : angle 2.39786 / 1.72 ( 32) hydrogen bonds : bond 0.04628 / 3.21 ( 410) hydrogen bonds : angle 4.96199 / 3.50 ( 1152) metal coordination : bond 0.00389 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.615 Fit side-chains REVERT: A 113 MET cc_start: 0.8690 (ttt) cc_final: 0.8360 (ttt) REVERT: A 134 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7327 (mp0) REVERT: A 330 LYS cc_start: 0.7904 (mttm) cc_final: 0.7570 (mtpp) REVERT: A 402 ASN cc_start: 0.8379 (t0) cc_final: 0.8136 (t0) REVERT: F 89 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7166 (mp0) REVERT: J 20 THR cc_start: 0.7034 (p) cc_final: 0.6683 (m) REVERT: J 54 ARG cc_start: 0.8273 (ttm110) cc_final: 0.8045 (ttm110) REVERT: J 88 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6945 (p) REVERT: J 90 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7617 (pp30) REVERT: B 113 MET cc_start: 0.8694 (ttt) cc_final: 0.8364 (ttt) REVERT: B 134 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7320 (mp0) REVERT: B 330 LYS cc_start: 0.7915 (mttm) cc_final: 0.7580 (mtpp) REVERT: B 402 ASN cc_start: 0.8389 (t0) cc_final: 0.8144 (t0) REVERT: D 89 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7158 (mp0) REVERT: H 20 THR cc_start: 0.7034 (p) cc_final: 0.6686 (m) REVERT: H 54 ARG cc_start: 0.8269 (ttm110) cc_final: 0.8040 (ttm110) REVERT: H 88 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6947 (p) REVERT: H 90 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7621 (pp30) outliers start: 48 outliers final: 34 residues processed: 230 average time/residue: 0.1238 time to fit residues: 42.9544 Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 119 optimal weight: 0.0370 chunk 180 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114096 restraints weight = 20141.170| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.47 r_work: 0.3279 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15524 Z= 0.101 Angle : 0.569 6.784 21052 Z= 0.299 Chirality : 0.046 0.189 2288 Planarity : 0.004 0.092 2698 Dihedral : 5.326 56.695 2130 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.68 % Allowed : 18.25 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.49 (0.19), residues: 1924 helix: 0.30 (0.31), residues: 296 sheet: -0.14 (0.23), residues: 548 loop : -1.90 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.017 0.001 TYR E 91 PHE 0.023 0.001 PHE B 380 TRP 0.012 0.001 TRP F 47 HIS 0.003 0.001 HIS J 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15502) covalent geometry : angle 0.56500 / 0.30 (21020) SS BOND : bond 0.00311 / 0.19 ( 16) SS BOND : angle 1.71329 / 1.23 ( 32) hydrogen bonds : bond 0.03171 / 2.18 ( 410) hydrogen bonds : angle 4.64038 / 3.28 ( 1152) metal coordination : bond 0.00152 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.643 Fit side-chains REVERT: A 46 GLU cc_start: 0.8152 (mp0) cc_final: 0.7470 (tt0) REVERT: A 113 MET cc_start: 0.8638 (ttt) cc_final: 0.8235 (ttt) REVERT: A 134 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7270 (mp0) REVERT: A 330 LYS cc_start: 0.7746 (mttm) cc_final: 0.7432 (mtpp) REVERT: A 402 ASN cc_start: 0.8326 (t0) cc_final: 0.8123 (t0) REVERT: A 497 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8383 (pp) REVERT: E 11 LEU cc_start: 0.7308 (mt) cc_final: 0.6843 (pp) REVERT: E 94 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6147 (t80) REVERT: F 89 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7240 (mp0) REVERT: I 20 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7165 (mt) REVERT: J 20 THR cc_start: 0.6931 (p) cc_final: 0.6536 (m) REVERT: J 103 LYS cc_start: 0.6757 (mtmt) cc_final: 0.6417 (mttt) REVERT: B 46 GLU cc_start: 0.8157 (mp0) cc_final: 0.7471 (tt0) REVERT: B 113 MET cc_start: 0.8657 (ttt) cc_final: 0.8261 (ttt) REVERT: B 134 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7252 (mp0) REVERT: B 330 LYS cc_start: 0.7755 (mttm) cc_final: 0.7440 (mtpp) REVERT: B 402 ASN cc_start: 0.8329 (t0) cc_final: 0.8124 (t0) REVERT: B 497 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 11 LEU cc_start: 0.7307 (mt) cc_final: 0.6848 (pp) REVERT: C 94 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6147 (t80) REVERT: D 89 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7221 (mp0) REVERT: G 20 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7159 (mt) REVERT: H 20 THR cc_start: 0.6937 (p) cc_final: 0.6541 (m) REVERT: H 103 LYS cc_start: 0.6762 (mtmt) cc_final: 0.6416 (mttt) outliers start: 44 outliers final: 32 residues processed: 224 average time/residue: 0.1279 time to fit residues: 43.1710 Evaluate side-chains 228 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 22 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 167 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111337 restraints weight = 20230.743| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.47 r_work: 0.3242 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15524 Z= 0.142 Angle : 0.613 7.427 21052 Z= 0.320 Chirality : 0.048 0.257 2288 Planarity : 0.005 0.092 2698 Dihedral : 5.452 55.953 2130 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.92 % Allowed : 18.13 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.44 (0.19), residues: 1924 helix: 0.35 (0.31), residues: 292 sheet: -0.07 (0.23), residues: 590 loop : -1.95 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.022 0.001 TYR C 91 PHE 0.021 0.001 PHE B 380 TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (15502) covalent geometry : angle 0.60780 / 0.32 (21020) SS BOND : bond 0.00398 / 0.24 ( 16) SS BOND : angle 2.04275 / 1.47 ( 32) hydrogen bonds : bond 0.03901 / 2.70 ( 410) hydrogen bonds : angle 4.67510 / 3.30 ( 1152) metal coordination : bond 0.00269 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.595 Fit side-chains REVERT: A 46 GLU cc_start: 0.8132 (mp0) cc_final: 0.7498 (tt0) REVERT: A 113 MET cc_start: 0.8681 (ttt) cc_final: 0.8295 (ttt) REVERT: A 134 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7256 (mp0) REVERT: A 330 LYS cc_start: 0.7762 (mttm) cc_final: 0.7450 (mtpp) REVERT: A 497 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8338 (pp) REVERT: E 11 LEU cc_start: 0.7312 (mt) cc_final: 0.6832 (pp) REVERT: E 94 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.6270 (t80) REVERT: F 89 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7220 (mp0) REVERT: J 20 THR cc_start: 0.6894 (p) cc_final: 0.6612 (m) REVERT: J 88 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6935 (p) REVERT: J 103 LYS cc_start: 0.6647 (mtmt) cc_final: 0.6284 (mttt) REVERT: B 46 GLU cc_start: 0.8141 (mp0) cc_final: 0.7489 (tt0) REVERT: B 113 MET cc_start: 0.8689 (ttt) cc_final: 0.8306 (ttt) REVERT: B 134 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7251 (mp0) REVERT: B 330 LYS cc_start: 0.7772 (mttm) cc_final: 0.7458 (mtpp) REVERT: B 497 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8335 (pp) REVERT: C 11 LEU cc_start: 0.7310 (mt) cc_final: 0.6832 (pp) REVERT: C 94 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.6271 (t80) REVERT: D 89 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7223 (mp0) REVERT: H 20 THR cc_start: 0.6904 (p) cc_final: 0.6623 (m) REVERT: H 88 CYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6937 (p) REVERT: H 103 LYS cc_start: 0.6669 (mtmt) cc_final: 0.6304 (mttt) outliers start: 48 outliers final: 34 residues processed: 220 average time/residue: 0.1256 time to fit residues: 41.3585 Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 170 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113047 restraints weight = 20314.722| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.48 r_work: 0.3281 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15524 Z= 0.111 Angle : 0.577 6.863 21052 Z= 0.303 Chirality : 0.046 0.204 2288 Planarity : 0.004 0.082 2698 Dihedral : 5.319 56.102 2130 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.92 % Allowed : 18.25 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.38 (0.19), residues: 1924 helix: 0.45 (0.31), residues: 296 sheet: 0.02 (0.23), residues: 548 loop : -1.90 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.018 0.001 TYR C 91 PHE 0.024 0.001 PHE A 380 TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS H 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15502) covalent geometry : angle 0.57302 / 0.30 (21020) SS BOND : bond 0.00324 / 0.21 ( 16) SS BOND : angle 1.88543 / 1.35 ( 32) hydrogen bonds : bond 0.03353 / 2.31 ( 410) hydrogen bonds : angle 4.57939 / 3.24 ( 1152) metal coordination : bond 0.00167 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.651 Fit side-chains REVERT: A 46 GLU cc_start: 0.8112 (mp0) cc_final: 0.7493 (tt0) REVERT: A 113 MET cc_start: 0.8651 (ttt) cc_final: 0.8255 (ttt) REVERT: A 134 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7268 (mp0) REVERT: A 330 LYS cc_start: 0.7774 (mttm) cc_final: 0.7465 (mtpp) REVERT: A 368 MET cc_start: 0.8622 (mtp) cc_final: 0.8421 (mtp) REVERT: A 379 MET cc_start: 0.8431 (tmm) cc_final: 0.7909 (tmm) REVERT: A 489 MET cc_start: 0.8539 (mmt) cc_final: 0.8042 (mmt) REVERT: A 497 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8340 (pp) REVERT: E 11 LEU cc_start: 0.7238 (mt) cc_final: 0.6810 (pp) REVERT: E 94 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.6228 (t80) REVERT: F 89 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7289 (mp0) REVERT: J 20 THR cc_start: 0.7049 (p) cc_final: 0.6725 (m) REVERT: J 88 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6885 (p) REVERT: J 103 LYS cc_start: 0.6510 (mtmt) cc_final: 0.6258 (mttt) REVERT: B 46 GLU cc_start: 0.8109 (mp0) cc_final: 0.7484 (tt0) REVERT: B 113 MET cc_start: 0.8670 (ttt) cc_final: 0.8279 (ttt) REVERT: B 134 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7258 (mp0) REVERT: B 330 LYS cc_start: 0.7779 (mttm) cc_final: 0.7470 (mtpp) REVERT: B 379 MET cc_start: 0.8408 (tmm) cc_final: 0.7887 (tmm) REVERT: B 489 MET cc_start: 0.8543 (mmt) cc_final: 0.8050 (mmt) REVERT: B 497 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8338 (pp) REVERT: C 11 LEU cc_start: 0.7236 (mt) cc_final: 0.6811 (pp) REVERT: C 94 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.6230 (t80) REVERT: D 89 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7290 (mp0) REVERT: H 20 THR cc_start: 0.7049 (p) cc_final: 0.6725 (m) REVERT: H 88 CYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6888 (p) REVERT: H 103 LYS cc_start: 0.6531 (mtmt) cc_final: 0.6275 (mttt) outliers start: 48 outliers final: 36 residues processed: 224 average time/residue: 0.1247 time to fit residues: 41.9978 Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 138 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 113 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN F 3 GLN I 35 HIS B 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109719 restraints weight = 20332.443| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.48 r_work: 0.3212 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15524 Z= 0.181 Angle : 0.660 7.847 21052 Z= 0.345 Chirality : 0.049 0.245 2288 Planarity : 0.005 0.091 2698 Dihedral : 5.601 55.441 2130 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.16 % Allowed : 18.55 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.51 (0.19), residues: 1924 helix: 0.25 (0.31), residues: 292 sheet: -0.03 (0.23), residues: 590 loop : -2.04 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 273 TYR 0.027 0.002 TYR C 94 PHE 0.022 0.002 PHE A 380 TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (15502) covalent geometry : angle 0.65327 / 0.34 (21020) SS BOND : bond 0.00413 / 0.25 ( 16) SS BOND : angle 2.42238 / 1.74 ( 32) hydrogen bonds : bond 0.04432 / 3.08 ( 410) hydrogen bonds : angle 4.77830 / 3.37 ( 1152) metal coordination : bond 0.00387 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.624 Fit side-chains REVERT: A 46 GLU cc_start: 0.8081 (mp0) cc_final: 0.7496 (tt0) REVERT: A 113 MET cc_start: 0.8711 (ttt) cc_final: 0.8373 (ttt) REVERT: A 134 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7196 (mp0) REVERT: A 330 LYS cc_start: 0.7800 (mttm) cc_final: 0.7484 (mtpp) REVERT: A 497 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8355 (pp) REVERT: E 11 LEU cc_start: 0.7296 (mt) cc_final: 0.6839 (pp) REVERT: E 94 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.6495 (t80) REVERT: F 89 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7280 (mp0) REVERT: J 20 THR cc_start: 0.6908 (p) cc_final: 0.6640 (m) REVERT: J 88 CYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6900 (p) REVERT: J 103 LYS cc_start: 0.6431 (mtmt) cc_final: 0.6158 (mttt) REVERT: B 46 GLU cc_start: 0.8075 (mp0) cc_final: 0.7484 (tt0) REVERT: B 113 MET cc_start: 0.8711 (ttt) cc_final: 0.8374 (ttt) REVERT: B 134 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7195 (mp0) REVERT: B 330 LYS cc_start: 0.7811 (mttm) cc_final: 0.7491 (mtpp) REVERT: B 497 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8347 (pp) REVERT: B 524 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8415 (p0) REVERT: C 11 LEU cc_start: 0.7293 (mt) cc_final: 0.6837 (pp) REVERT: C 94 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.6492 (t80) REVERT: D 89 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7277 (mp0) REVERT: H 20 THR cc_start: 0.6914 (p) cc_final: 0.6645 (m) REVERT: H 88 CYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6894 (p) REVERT: H 103 LYS cc_start: 0.6449 (mtmt) cc_final: 0.6173 (mttt) outliers start: 52 outliers final: 38 residues processed: 230 average time/residue: 0.1251 time to fit residues: 43.2790 Evaluate side-chains 235 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 1.9990 chunk 145 optimal weight: 0.0030 chunk 169 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.0010 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN B 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.146978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112686 restraints weight = 20342.558| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.48 r_work: 0.3251 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15524 Z= 0.114 Angle : 0.595 6.900 21052 Z= 0.313 Chirality : 0.047 0.221 2288 Planarity : 0.004 0.078 2698 Dihedral : 5.394 55.947 2130 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.86 % Allowed : 18.98 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.38 (0.19), residues: 1924 helix: 0.42 (0.31), residues: 296 sheet: 0.10 (0.23), residues: 572 loop : -1.98 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.019 0.001 TYR C 91 PHE 0.025 0.001 PHE A 380 TRP 0.013 0.001 TRP F 47 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (15502) covalent geometry : angle 0.59020 / 0.31 (21020) SS BOND : bond 0.00339 / 0.21 ( 16) SS BOND : angle 1.92394 / 1.38 ( 32) hydrogen bonds : bond 0.03413 / 2.36 ( 410) hydrogen bonds : angle 4.60674 / 3.26 ( 1152) metal coordination : bond 0.00195 / 0.11 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.564 Fit side-chains REVERT: A 46 GLU cc_start: 0.8023 (mp0) cc_final: 0.7469 (tt0) REVERT: A 113 MET cc_start: 0.8676 (ttt) cc_final: 0.8293 (ttt) REVERT: A 134 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7209 (mp0) REVERT: A 330 LYS cc_start: 0.7752 (mttm) cc_final: 0.7441 (mtpp) REVERT: A 379 MET cc_start: 0.8512 (tmm) cc_final: 0.8007 (tmm) REVERT: A 489 MET cc_start: 0.8497 (mmt) cc_final: 0.7942 (mmt) REVERT: A 497 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8350 (pp) REVERT: E 11 LEU cc_start: 0.7267 (mt) cc_final: 0.6862 (pp) REVERT: E 94 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.6307 (t80) REVERT: F 89 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7293 (mp0) REVERT: J 20 THR cc_start: 0.6904 (p) cc_final: 0.6686 (m) REVERT: J 88 CYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6836 (p) REVERT: J 103 LYS cc_start: 0.6497 (mtmt) cc_final: 0.6251 (mttt) REVERT: B 46 GLU cc_start: 0.8026 (mp0) cc_final: 0.7466 (tt0) REVERT: B 113 MET cc_start: 0.8685 (ttt) cc_final: 0.8298 (ttt) REVERT: B 134 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7203 (mp0) REVERT: B 330 LYS cc_start: 0.7756 (mttm) cc_final: 0.7443 (mtpp) REVERT: B 379 MET cc_start: 0.8490 (tmm) cc_final: 0.7982 (tmm) REVERT: B 489 MET cc_start: 0.8504 (mmt) cc_final: 0.7950 (mmt) REVERT: B 497 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8385 (pp) REVERT: C 11 LEU cc_start: 0.7263 (mt) cc_final: 0.6863 (pp) REVERT: C 94 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.6321 (t80) REVERT: D 89 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7295 (mp0) REVERT: H 20 THR cc_start: 0.6908 (p) cc_final: 0.6688 (m) REVERT: H 88 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6835 (p) REVERT: H 103 LYS cc_start: 0.6500 (mtmt) cc_final: 0.6257 (mttt) outliers start: 47 outliers final: 38 residues processed: 225 average time/residue: 0.1203 time to fit residues: 40.6915 Evaluate side-chains 232 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 ASN B 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110552 restraints weight = 20015.303| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.38 r_work: 0.3229 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15524 Z= 0.169 Angle : 0.642 7.531 21052 Z= 0.335 Chirality : 0.049 0.248 2288 Planarity : 0.005 0.086 2698 Dihedral : 5.507 55.533 2130 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.86 % Allowed : 19.04 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % 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: -1.45 (0.19), residues: 1924 helix: 0.34 (0.31), residues: 292 sheet: 0.06 (0.23), residues: 576 loop : -2.02 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.025 0.002 TYR E 91 PHE 0.025 0.002 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.005 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (15502) covalent geometry : angle 0.63578 / 0.33 (21020) SS BOND : bond 0.00404 / 0.25 ( 16) SS BOND : angle 2.29525 / 1.63 ( 32) hydrogen bonds : bond 0.04145 / 2.88 ( 410) hydrogen bonds : angle 4.69270 / 3.31 ( 1152) metal coordination : bond 0.00361 / 0.21 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4524.05 seconds wall clock time: 78 minutes 17.47 seconds (4697.47 seconds total)