Starting phenix.real_space_refine on Fri Jun 13 14:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znz_60281/06_2025/8znz_60281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znz_60281/06_2025/8znz_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_60281/06_2025/8znz_60281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znz_60281/06_2025/8znz_60281.map" model { file = "/net/cci-nas-00/data/ceres_data/8znz_60281/06_2025/8znz_60281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znz_60281/06_2025/8znz_60281.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "C" 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: "D" 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: "G" 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: "H" 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, 4 Unusual residues: {' CA': 1, ' NA': 1, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: J, E, B, I, F Time building chain proxies: 14.01, per 1000 atoms: 0.92 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=12, 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 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: 3.74 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.07 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: 5.14 Time building geometry restraints manager: 4.46 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: 8027 17.89 - 35.79: 885 35.79 - 53.68: 194 53.68 - 71.58: 44 71.58 - 89.47: 20 Dihedral angle restraints: 9170 sinusoidal: 3596 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 9167 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: 2.03 - 2.61: 222 2.61 - 3.18: 12860 3.18 - 3.75: 20496 3.75 - 4.33: 30924 4.33 - 4.90: 53659 Nonbonded interactions: 118161 Sorted by model distance: nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " model vdw 2.035 3.760 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=" SG CYS H 23 " pdb=" SG CYS H 88 " model vdw 2.060 3.760 ... (remaining 118156 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: 0.08 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 10.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.090 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 15520 Z= 0.489 Angle : 1.038 13.882 21044 Z= 0.660 Chirality : 0.077 0.634 2288 Planarity : 0.027 0.494 2698 Dihedral : 16.228 89.470 5602 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP D 47 HIS 0.007 0.002 HIS B 383 PHE 0.020 0.004 PHE A 183 TYR 0.047 0.005 TYR J 94 ARG 0.016 0.002 ARG A 401 Details of bonding type rmsd hydrogen bonds : bond 0.23461 ( 410) hydrogen bonds : angle 9.18213 ( 1152) metal coordination : bond 0.27287 ( 6) SS BOND : bond 0.02266 ( 12) SS BOND : angle 2.84943 ( 24) covalent geometry : bond 0.00798 (15502) covalent geometry : angle 1.03440 (21020) *********************** 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 : 1.622 Fit side-chains REVERT: A 87 TYR cc_start: 0.8203 (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: 0.2812 time to fit residues: 96.0573 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 : 1.600 ------------------------------------------------------------------------------- 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 160 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 88 GLN I 52 HIS J 79 GLN B 69 GLN B 88 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3828 r_free = 0.3828 target = 0.147257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114173 restraints weight = 19932.743| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.41 r_work: 0.3278 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15520 Z= 0.162 Angle : 0.721 12.089 21044 Z= 0.377 Chirality : 0.051 0.273 2288 Planarity : 0.005 0.094 2698 Dihedral : 5.821 54.710 2130 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.70 % Allowed : 11.19 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.18), residues: 1924 helix: -0.66 (0.29), residues: 290 sheet: -0.91 (0.22), residues: 608 loop : -2.50 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 47 HIS 0.004 0.001 HIS B 383 PHE 0.019 0.002 PHE J 71 TYR 0.025 0.002 TYR C 91 ARG 0.007 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 410) hydrogen bonds : angle 5.84341 ( 1152) metal coordination : bond 0.01119 ( 6) SS BOND : bond 0.00604 ( 12) SS BOND : angle 3.50912 ( 24) covalent geometry : bond 0.00381 (15502) covalent geometry : angle 0.71122 (21020) *********************** 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 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.768 Fit side-chains REVERT: A 134 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7295 (mm-30) REVERT: A 330 LYS cc_start: 0.7880 (mttm) cc_final: 0.7506 (mtpp) REVERT: I 50 MET cc_start: 0.8363 (mtt) cc_final: 0.8061 (mtm) REVERT: I 105 GLU cc_start: 0.7703 (mp0) cc_final: 0.7432 (mp0) REVERT: J 20 THR cc_start: 0.6890 (p) cc_final: 0.6359 (m) REVERT: J 94 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6241 (t80) REVERT: B 134 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7286 (mm-30) REVERT: B 330 LYS cc_start: 0.7869 (mttm) cc_final: 0.7494 (mtpp) REVERT: C 4 MET cc_start: 0.8590 (mmm) cc_final: 0.8048 (tpt) REVERT: G 50 MET cc_start: 0.8379 (mtt) cc_final: 0.8072 (mtm) REVERT: G 105 GLU cc_start: 0.7688 (mp0) cc_final: 0.7416 (mp0) REVERT: H 20 THR cc_start: 0.6934 (p) cc_final: 0.6388 (m) REVERT: H 94 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6243 (t80) outliers start: 28 outliers final: 22 residues processed: 232 average time/residue: 0.2791 time to fit residues: 95.6486 Evaluate side-chains 223 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 256 LYS 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 256 LYS 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 119 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111768 restraints weight = 20077.297| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.44 r_work: 0.3247 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15520 Z= 0.157 Angle : 0.650 8.289 21044 Z= 0.341 Chirality : 0.049 0.220 2288 Planarity : 0.005 0.096 2698 Dihedral : 5.692 53.659 2130 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.95 % Allowed : 14.29 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.18), residues: 1924 helix: -0.47 (0.29), residues: 296 sheet: -0.68 (0.23), residues: 580 loop : -2.26 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS B 383 PHE 0.020 0.002 PHE B 380 TYR 0.022 0.002 TYR C 91 ARG 0.004 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 410) hydrogen bonds : angle 5.30512 ( 1152) metal coordination : bond 0.00215 ( 6) SS BOND : bond 0.00518 ( 12) SS BOND : angle 2.67041 ( 24) covalent geometry : bond 0.00382 (15502) covalent geometry : angle 0.64451 (21020) *********************** 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 230 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.784 Fit side-chains REVERT: A 113 MET cc_start: 0.8629 (ttt) cc_final: 0.8294 (ttt) REVERT: A 330 LYS cc_start: 0.7884 (mttm) cc_final: 0.7524 (mtpp) REVERT: A 379 MET cc_start: 0.8489 (tmm) cc_final: 0.8156 (tmm) REVERT: I 50 MET cc_start: 0.8347 (mtt) cc_final: 0.8091 (mtm) REVERT: J 20 THR cc_start: 0.6915 (p) cc_final: 0.6411 (m) REVERT: J 90 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7371 (pp30) REVERT: J 94 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6486 (t80) REVERT: B 330 LYS cc_start: 0.7894 (mttm) cc_final: 0.7533 (mtpp) REVERT: B 379 MET cc_start: 0.8494 (tmm) cc_final: 0.8161 (tmm) REVERT: G 50 MET cc_start: 0.8373 (mtt) cc_final: 0.8079 (mtm) REVERT: H 20 THR cc_start: 0.6947 (p) cc_final: 0.6465 (m) REVERT: H 90 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7386 (pp30) REVERT: H 94 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6412 (t80) outliers start: 32 outliers final: 23 residues processed: 212 average time/residue: 0.2885 time to fit residues: 90.2578 Evaluate side-chains 223 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 256 LYS Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 71 SER 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 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 256 LYS Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 71 SER 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 5 THR 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 55 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 213 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110046 restraints weight = 20087.952| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.38 r_work: 0.3248 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15520 Z= 0.156 Angle : 0.636 7.623 21044 Z= 0.333 Chirality : 0.048 0.198 2288 Planarity : 0.005 0.098 2698 Dihedral : 5.661 54.809 2130 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.55 % Allowed : 16.00 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1924 helix: -0.21 (0.30), residues: 296 sheet: -0.52 (0.23), residues: 580 loop : -2.16 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS A 383 PHE 0.019 0.002 PHE B 380 TYR 0.023 0.002 TYR C 91 ARG 0.004 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 410) hydrogen bonds : angle 5.06661 ( 1152) metal coordination : bond 0.00343 ( 6) SS BOND : bond 0.00448 ( 12) SS BOND : angle 2.54708 ( 24) covalent geometry : bond 0.00386 (15502) covalent geometry : angle 0.63094 (21020) *********************** 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 240 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.756 Fit side-chains REVERT: A 113 MET cc_start: 0.8697 (ttt) cc_final: 0.8362 (ttt) REVERT: A 134 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7308 (mp0) REVERT: A 330 LYS cc_start: 0.7844 (mttm) cc_final: 0.7495 (mtpp) REVERT: F 89 GLU cc_start: 0.7220 (mp0) cc_final: 0.7015 (mt-10) REVERT: I 105 GLU cc_start: 0.7565 (mp0) cc_final: 0.7252 (mp0) REVERT: J 20 THR cc_start: 0.6907 (p) cc_final: 0.6641 (m) REVERT: J 88 CYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6878 (p) REVERT: J 90 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7494 (pp30) REVERT: B 113 MET cc_start: 0.8710 (ttt) cc_final: 0.8377 (ttt) REVERT: B 134 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7292 (mp0) REVERT: B 330 LYS cc_start: 0.7868 (mttm) cc_final: 0.7517 (mtpp) REVERT: D 89 GLU cc_start: 0.7216 (mp0) cc_final: 0.7010 (mt-10) REVERT: G 30 THR cc_start: 0.8541 (m) cc_final: 0.8333 (t) REVERT: G 105 GLU cc_start: 0.7566 (mp0) cc_final: 0.7248 (mp0) REVERT: H 20 THR cc_start: 0.6863 (p) cc_final: 0.6560 (m) REVERT: H 90 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7509 (pp30) outliers start: 42 outliers final: 30 residues processed: 225 average time/residue: 0.2664 time to fit residues: 88.7027 Evaluate side-chains 225 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 256 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain E residue 5 THR 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 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 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU 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 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 148 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108450 restraints weight = 20429.384| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.44 r_work: 0.3205 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15520 Z= 0.174 Angle : 0.646 7.857 21044 Z= 0.337 Chirality : 0.049 0.224 2288 Planarity : 0.005 0.101 2698 Dihedral : 5.754 57.703 2130 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.71 % Allowed : 16.91 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1924 helix: -0.10 (0.30), residues: 292 sheet: -0.36 (0.23), residues: 592 loop : -2.15 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS B 383 PHE 0.018 0.002 PHE B 380 TYR 0.025 0.002 TYR H 94 ARG 0.003 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 410) hydrogen bonds : angle 4.99626 ( 1152) metal coordination : bond 0.00386 ( 6) SS BOND : bond 0.00492 ( 12) SS BOND : angle 2.50295 ( 24) covalent geometry : bond 0.00432 (15502) covalent geometry : angle 0.64078 (21020) *********************** 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 257 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 1.647 Fit side-chains REVERT: A 113 MET cc_start: 0.8724 (ttt) cc_final: 0.8383 (ttt) REVERT: A 134 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7301 (mp0) REVERT: A 330 LYS cc_start: 0.7838 (mttm) cc_final: 0.7512 (mtpp) REVERT: E 11 LEU cc_start: 0.7284 (mt) cc_final: 0.6773 (pp) REVERT: E 94 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6319 (t80) REVERT: J 20 THR cc_start: 0.7025 (p) cc_final: 0.6674 (m) REVERT: J 88 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6869 (p) REVERT: J 90 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7643 (pp30) REVERT: B 113 MET cc_start: 0.8730 (ttt) cc_final: 0.8390 (ttt) REVERT: B 134 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7292 (mp0) REVERT: B 330 LYS cc_start: 0.7852 (mttm) cc_final: 0.7525 (mtpp) REVERT: C 11 LEU cc_start: 0.7292 (mt) cc_final: 0.6782 (pp) REVERT: C 94 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.6309 (t80) REVERT: H 20 THR cc_start: 0.7037 (p) cc_final: 0.6673 (m) REVERT: H 90 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7680 (pp30) REVERT: H 103 LYS cc_start: 0.6672 (mtmt) cc_final: 0.6307 (mttt) outliers start: 61 outliers final: 39 residues processed: 241 average time/residue: 0.2734 time to fit residues: 97.6834 Evaluate side-chains 234 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 256 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 75 ILE 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 91 THR 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 83 LEU 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 256 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR 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 5 THR Chi-restraints excluded: chain H residue 15 VAL 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 146 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109950 restraints weight = 20212.897| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.46 r_work: 0.3222 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15520 Z= 0.148 Angle : 0.624 7.441 21044 Z= 0.326 Chirality : 0.048 0.213 2288 Planarity : 0.005 0.099 2698 Dihedral : 5.636 57.728 2130 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.22 % Allowed : 18.31 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1924 helix: 0.06 (0.31), residues: 292 sheet: -0.29 (0.23), residues: 594 loop : -2.09 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS B 383 PHE 0.020 0.001 PHE A 380 TYR 0.022 0.002 TYR J 94 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 410) hydrogen bonds : angle 4.84939 ( 1152) metal coordination : bond 0.00312 ( 6) SS BOND : bond 0.00391 ( 12) SS BOND : angle 2.36775 ( 24) covalent geometry : bond 0.00367 (15502) covalent geometry : angle 0.61903 (21020) *********************** 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 250 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.691 Fit side-chains REVERT: A 46 GLU cc_start: 0.8134 (mp0) cc_final: 0.7582 (tt0) REVERT: A 113 MET cc_start: 0.8708 (ttt) cc_final: 0.8338 (ttt) REVERT: A 134 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7244 (mp0) REVERT: A 330 LYS cc_start: 0.7806 (mttm) cc_final: 0.7463 (mtpp) REVERT: A 402 ASN cc_start: 0.8257 (t0) cc_final: 0.7984 (t0) REVERT: A 497 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8402 (pp) REVERT: E 11 LEU cc_start: 0.7288 (mt) cc_final: 0.6776 (pp) REVERT: E 94 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.6369 (t80) REVERT: F 43 LYS cc_start: 0.7776 (mtpp) cc_final: 0.7394 (mttp) REVERT: I 105 GLU cc_start: 0.7528 (mp0) cc_final: 0.7218 (mp0) REVERT: J 20 THR cc_start: 0.6950 (p) cc_final: 0.6674 (m) REVERT: J 88 CYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6838 (p) REVERT: J 90 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7640 (pp30) REVERT: B 46 GLU cc_start: 0.8126 (mp0) cc_final: 0.7570 (tt0) REVERT: B 113 MET cc_start: 0.8719 (ttt) cc_final: 0.8355 (ttt) REVERT: B 134 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7241 (mp0) REVERT: B 330 LYS cc_start: 0.7832 (mttm) cc_final: 0.7487 (mtpp) REVERT: B 402 ASN cc_start: 0.8251 (t0) cc_final: 0.7980 (t0) REVERT: B 497 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8401 (pp) REVERT: C 11 LEU cc_start: 0.7291 (mt) cc_final: 0.6791 (pp) REVERT: C 94 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.6242 (t80) REVERT: G 105 GLU cc_start: 0.7551 (mp0) cc_final: 0.7238 (mp0) REVERT: H 20 THR cc_start: 0.7108 (p) cc_final: 0.6771 (m) REVERT: H 103 LYS cc_start: 0.6726 (mtmt) cc_final: 0.6367 (mttt) outliers start: 53 outliers final: 36 residues processed: 240 average time/residue: 0.2668 time to fit residues: 95.1864 Evaluate side-chains 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 256 LYS 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 75 ILE 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 23 CYS 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 256 LYS 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 75 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU 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 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 161 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 62 optimal weight: 0.0370 chunk 166 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112247 restraints weight = 20370.066| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.47 r_work: 0.3246 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15520 Z= 0.109 Angle : 0.577 6.968 21044 Z= 0.301 Chirality : 0.046 0.251 2288 Planarity : 0.004 0.089 2698 Dihedral : 5.420 58.172 2130 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.68 % Allowed : 19.71 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1924 helix: 0.38 (0.31), residues: 292 sheet: -0.08 (0.23), residues: 576 loop : -1.94 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.004 0.001 HIS H 91 PHE 0.021 0.001 PHE A 380 TYR 0.017 0.001 TYR J 94 ARG 0.003 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 410) hydrogen bonds : angle 4.66689 ( 1152) metal coordination : bond 0.00177 ( 6) SS BOND : bond 0.00352 ( 12) SS BOND : angle 2.10939 ( 24) covalent geometry : bond 0.00260 (15502) covalent geometry : angle 0.57255 (21020) *********************** 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 247 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 1.797 Fit side-chains REVERT: A 46 GLU cc_start: 0.8125 (mp0) cc_final: 0.7430 (tt0) REVERT: A 113 MET cc_start: 0.8689 (ttt) cc_final: 0.8314 (ttt) REVERT: A 134 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7242 (mp0) REVERT: A 312 SER cc_start: 0.8091 (t) cc_final: 0.7852 (p) REVERT: A 330 LYS cc_start: 0.7744 (mttm) cc_final: 0.7443 (mtpp) REVERT: A 379 MET cc_start: 0.8517 (tmm) cc_final: 0.7992 (tmm) REVERT: A 402 ASN cc_start: 0.8273 (t0) cc_final: 0.7953 (t0) REVERT: A 497 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8413 (pp) REVERT: E 11 LEU cc_start: 0.7311 (mt) cc_final: 0.6810 (pp) REVERT: E 94 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6337 (t80) REVERT: F 89 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7229 (mp0) REVERT: I 20 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7235 (mt) REVERT: I 30 THR cc_start: 0.8599 (m) cc_final: 0.8390 (t) REVERT: I 105 GLU cc_start: 0.7553 (mp0) cc_final: 0.7292 (mp0) REVERT: J 20 THR cc_start: 0.6818 (p) cc_final: 0.6574 (m) REVERT: J 88 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6723 (p) REVERT: J 103 LYS cc_start: 0.6622 (mtmt) cc_final: 0.6348 (mttt) REVERT: B 46 GLU cc_start: 0.8125 (mp0) cc_final: 0.7423 (tt0) REVERT: B 113 MET cc_start: 0.8708 (ttt) cc_final: 0.8339 (ttt) REVERT: B 134 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7240 (mp0) REVERT: B 312 SER cc_start: 0.8092 (t) cc_final: 0.7855 (p) REVERT: B 330 LYS cc_start: 0.7757 (mttm) cc_final: 0.7457 (mtpp) REVERT: B 379 MET cc_start: 0.8490 (tmm) cc_final: 0.7966 (tmm) REVERT: B 402 ASN cc_start: 0.8261 (t0) cc_final: 0.7947 (t0) REVERT: B 497 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8409 (pp) REVERT: C 11 LEU cc_start: 0.7319 (mt) cc_final: 0.6827 (pp) REVERT: C 94 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6259 (t80) REVERT: D 89 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7225 (mp0) REVERT: G 105 GLU cc_start: 0.7521 (mp0) cc_final: 0.7257 (mp0) REVERT: H 20 THR cc_start: 0.7006 (p) cc_final: 0.6710 (m) REVERT: H 103 LYS cc_start: 0.6656 (mtmt) cc_final: 0.6284 (mttt) outliers start: 44 outliers final: 30 residues processed: 234 average time/residue: 0.2786 time to fit residues: 97.2033 Evaluate side-chains 229 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 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 94 TYR Chi-restraints excluded: chain F residue 20 LEU 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 83 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 69 THR 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 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 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 79 LEU 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 94 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 213 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109298 restraints weight = 20130.539| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.39 r_work: 0.3209 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15520 Z= 0.166 Angle : 0.636 7.792 21044 Z= 0.330 Chirality : 0.048 0.215 2288 Planarity : 0.005 0.093 2698 Dihedral : 5.607 57.585 2130 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.80 % Allowed : 19.77 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1924 helix: 0.25 (0.31), residues: 292 sheet: -0.07 (0.23), residues: 576 loop : -2.06 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 47 HIS 0.005 0.001 HIS B 383 PHE 0.021 0.002 PHE A 380 TYR 0.026 0.002 TYR E 94 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 410) hydrogen bonds : angle 4.77538 ( 1152) metal coordination : bond 0.00366 ( 6) SS BOND : bond 0.00410 ( 12) SS BOND : angle 2.55698 ( 24) covalent geometry : bond 0.00413 (15502) covalent geometry : angle 0.63016 (21020) *********************** 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 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.900 Fit side-chains REVERT: A 46 GLU cc_start: 0.8097 (mp0) cc_final: 0.7512 (tt0) REVERT: A 113 MET cc_start: 0.8728 (ttt) cc_final: 0.8375 (ttt) REVERT: A 134 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7239 (mp0) REVERT: A 330 LYS cc_start: 0.7787 (mttm) cc_final: 0.7472 (mtpp) REVERT: A 402 ASN cc_start: 0.8289 (t0) cc_final: 0.7970 (t0) REVERT: A 497 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8374 (pp) REVERT: E 11 LEU cc_start: 0.7335 (mt) cc_final: 0.6830 (pp) REVERT: E 94 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.6472 (t80) REVERT: F 89 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7268 (mp0) REVERT: J 20 THR cc_start: 0.6871 (p) cc_final: 0.6602 (m) REVERT: J 88 CYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6801 (p) REVERT: J 103 LYS cc_start: 0.6775 (mtmt) cc_final: 0.6483 (mttt) REVERT: B 46 GLU cc_start: 0.8105 (mp0) cc_final: 0.7521 (tt0) REVERT: B 113 MET cc_start: 0.8723 (ttt) cc_final: 0.8372 (ttt) REVERT: B 134 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7232 (mp0) REVERT: B 330 LYS cc_start: 0.7804 (mttm) cc_final: 0.7487 (mtpp) REVERT: B 402 ASN cc_start: 0.8286 (t0) cc_final: 0.7973 (t0) REVERT: B 497 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8373 (pp) REVERT: C 11 LEU cc_start: 0.7325 (mt) cc_final: 0.6827 (pp) REVERT: C 94 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.6392 (t80) REVERT: D 89 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7266 (mp0) REVERT: H 20 THR cc_start: 0.7029 (p) cc_final: 0.6709 (m) REVERT: H 103 LYS cc_start: 0.6715 (mtmt) cc_final: 0.6348 (mttt) outliers start: 46 outliers final: 34 residues processed: 232 average time/residue: 0.3077 time to fit residues: 107.0500 Evaluate side-chains 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 75 ILE 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 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 15 VAL Chi-restraints excluded: chain J residue 23 CYS 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 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 79 LEU 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 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 97 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 152 optimal weight: 0.2980 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 0.0170 chunk 96 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 213 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111753 restraints weight = 20271.676| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.48 r_work: 0.3243 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15520 Z= 0.112 Angle : 0.586 6.944 21044 Z= 0.306 Chirality : 0.046 0.250 2288 Planarity : 0.004 0.084 2698 Dihedral : 5.413 57.255 2130 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.49 % Allowed : 20.07 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1924 helix: 0.39 (0.31), residues: 296 sheet: -0.03 (0.23), residues: 562 loop : -1.96 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 47 HIS 0.003 0.001 HIS H 91 PHE 0.025 0.001 PHE B 380 TYR 0.017 0.001 TYR H 94 ARG 0.002 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 410) hydrogen bonds : angle 4.61638 ( 1152) metal coordination : bond 0.00174 ( 6) SS BOND : bond 0.00311 ( 12) SS BOND : angle 2.11485 ( 24) covalent geometry : bond 0.00270 (15502) covalent geometry : angle 0.58182 (21020) *********************** 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 235 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.776 Fit side-chains REVERT: A 46 GLU cc_start: 0.8023 (mp0) cc_final: 0.7487 (tt0) REVERT: A 113 MET cc_start: 0.8689 (ttt) cc_final: 0.8313 (ttt) REVERT: A 134 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7219 (mp0) REVERT: A 312 SER cc_start: 0.8072 (t) cc_final: 0.7829 (p) REVERT: A 330 LYS cc_start: 0.7747 (mttm) cc_final: 0.7451 (mtpp) REVERT: A 379 MET cc_start: 0.8495 (tmm) cc_final: 0.8025 (tmm) REVERT: A 402 ASN cc_start: 0.8255 (t0) cc_final: 0.7918 (t0) REVERT: A 489 MET cc_start: 0.8569 (mmt) cc_final: 0.7979 (mmt) REVERT: A 497 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8371 (pp) REVERT: E 11 LEU cc_start: 0.7334 (mt) cc_final: 0.6835 (pp) REVERT: E 94 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.6272 (t80) REVERT: F 89 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7261 (mp0) REVERT: J 20 THR cc_start: 0.6821 (p) cc_final: 0.6615 (m) REVERT: J 88 CYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6686 (p) REVERT: J 103 LYS cc_start: 0.6806 (mtmt) cc_final: 0.6513 (mttt) REVERT: B 46 GLU cc_start: 0.8024 (mp0) cc_final: 0.7487 (tt0) REVERT: B 113 MET cc_start: 0.8695 (ttt) cc_final: 0.8319 (ttt) REVERT: B 134 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7215 (mp0) REVERT: B 312 SER cc_start: 0.8071 (t) cc_final: 0.7828 (p) REVERT: B 330 LYS cc_start: 0.7762 (mttm) cc_final: 0.7464 (mtpp) REVERT: B 379 MET cc_start: 0.8466 (tmm) cc_final: 0.7997 (tmm) REVERT: B 402 ASN cc_start: 0.8233 (t0) cc_final: 0.7903 (t0) REVERT: B 489 MET cc_start: 0.8566 (mmt) cc_final: 0.7976 (mmt) REVERT: B 497 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 11 LEU cc_start: 0.7318 (mt) cc_final: 0.6835 (pp) REVERT: C 94 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.6280 (t80) REVERT: D 89 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7256 (mp0) REVERT: H 20 THR cc_start: 0.7096 (p) cc_final: 0.6800 (m) REVERT: H 103 LYS cc_start: 0.6740 (mtmt) cc_final: 0.6383 (mttt) outliers start: 41 outliers final: 32 residues processed: 225 average time/residue: 0.2750 time to fit residues: 92.1002 Evaluate side-chains 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 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 94 TYR Chi-restraints excluded: chain F residue 20 LEU 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 69 THR 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 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 75 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 79 LEU 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 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 8 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109721 restraints weight = 20180.847| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.40 r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15520 Z= 0.145 Angle : 0.619 7.438 21044 Z= 0.322 Chirality : 0.048 0.267 2288 Planarity : 0.005 0.088 2698 Dihedral : 5.493 56.910 2130 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.55 % Allowed : 20.26 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1924 helix: 0.41 (0.31), residues: 292 sheet: 0.05 (0.23), residues: 576 loop : -2.01 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 47 HIS 0.004 0.001 HIS A 383 PHE 0.025 0.001 PHE B 380 TYR 0.022 0.001 TYR E 94 ARG 0.002 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 410) hydrogen bonds : angle 4.65415 ( 1152) metal coordination : bond 0.00296 ( 6) SS BOND : bond 0.00374 ( 12) SS BOND : angle 2.39736 ( 24) covalent geometry : bond 0.00359 (15502) covalent geometry : angle 0.61371 (21020) ********************** 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: 42 poor density : 193 time to evaluate : 1.687 Fit side-chains REVERT: A 46 GLU cc_start: 0.8030 (mp0) cc_final: 0.7489 (tt0) REVERT: A 113 MET cc_start: 0.8696 (ttt) cc_final: 0.8332 (ttt) REVERT: A 134 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7192 (mp0) REVERT: A 312 SER cc_start: 0.8035 (t) cc_final: 0.7788 (p) REVERT: A 330 LYS cc_start: 0.7760 (mttm) cc_final: 0.7465 (mtpp) REVERT: A 379 MET cc_start: 0.8478 (tmm) cc_final: 0.8001 (tmm) REVERT: A 402 ASN cc_start: 0.8287 (t0) cc_final: 0.7954 (t0) REVERT: A 497 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8366 (pp) REVERT: E 11 LEU cc_start: 0.7316 (mt) cc_final: 0.6821 (pp) REVERT: E 94 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6324 (t80) REVERT: F 89 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7263 (mp0) REVERT: J 20 THR cc_start: 0.6868 (p) cc_final: 0.6622 (m) REVERT: J 88 CYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6757 (p) REVERT: J 103 LYS cc_start: 0.6818 (mtmt) cc_final: 0.6534 (mttt) REVERT: B 46 GLU cc_start: 0.8047 (mp0) cc_final: 0.7493 (tt0) REVERT: B 113 MET cc_start: 0.8712 (ttt) cc_final: 0.8350 (ttt) REVERT: B 134 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7178 (mp0) REVERT: B 312 SER cc_start: 0.8034 (t) cc_final: 0.7787 (p) REVERT: B 330 LYS cc_start: 0.7778 (mttm) cc_final: 0.7479 (mtpp) REVERT: B 379 MET cc_start: 0.8463 (tmm) cc_final: 0.7997 (tmm) REVERT: B 402 ASN cc_start: 0.8282 (t0) cc_final: 0.7952 (t0) REVERT: B 497 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 11 LEU cc_start: 0.7316 (mt) cc_final: 0.6828 (pp) REVERT: C 94 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6321 (t80) REVERT: D 89 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7269 (mp0) REVERT: H 20 THR cc_start: 0.7108 (p) cc_final: 0.6823 (m) REVERT: H 103 LYS cc_start: 0.6781 (mtmt) cc_final: 0.6409 (mttt) outliers start: 42 outliers final: 34 residues processed: 224 average time/residue: 0.2695 time to fit residues: 90.1967 Evaluate side-chains 232 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 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 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 75 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR 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 48 ILE 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 141 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110838 restraints weight = 20267.400| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.48 r_work: 0.3228 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15520 Z= 0.136 Angle : 0.609 7.165 21044 Z= 0.317 Chirality : 0.047 0.251 2288 Planarity : 0.005 0.084 2698 Dihedral : 5.465 56.830 2130 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.68 % Allowed : 20.13 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 1924 helix: 0.43 (0.31), residues: 292 sheet: 0.08 (0.23), residues: 576 loop : -1.96 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 47 HIS 0.004 0.001 HIS A 383 PHE 0.025 0.001 PHE B 380 TYR 0.020 0.001 TYR E 91 ARG 0.002 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 410) hydrogen bonds : angle 4.62923 ( 1152) metal coordination : bond 0.00267 ( 6) SS BOND : bond 0.00326 ( 12) SS BOND : angle 2.31295 ( 24) covalent geometry : bond 0.00335 (15502) covalent geometry : angle 0.60419 (21020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9424.01 seconds wall clock time: 161 minutes 54.53 seconds (9714.53 seconds total)