Starting phenix.real_space_refine on Thu Sep 18 07:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znz_60281/09_2025/8znz_60281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znz_60281/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8znz_60281/09_2025/8znz_60281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znz_60281/09_2025/8znz_60281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znz_60281/09_2025/8znz_60281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znz_60281/09_2025/8znz_60281.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 4 6.06 5 S 70 5.16 5 Na 2 4.78 5 C 9618 2.51 5 N 2566 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 184 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15154 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4089 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 796 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 957 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 1, ' NA': 1, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D, G, H Time building chain proxies: 4.80, per 1000 atoms: 0.32 Number of scatterers: 15154 At special positions: 0 Unit cell: (148.05, 126.054, 115.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 2 19.99 S 70 16.00 Na 2 11.00 O 2892 8.00 N 2566 7.00 C 9618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 57 " distance=2.02 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 358 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 387 " distance=2.07 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 479 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.08 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.06 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 57 " distance=2.02 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 358 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 387 " distance=2.07 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 479 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.08 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 769.6 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 220 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 243 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 38 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 220 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 243 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 38 " 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 32 sheets defined 19.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 60 through 75 removed outlier: 3.664A pdb=" N LEU A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.628A pdb=" N VAL A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 123 through 129 removed outlier: 4.070A pdb=" N GLU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.835A pdb=" N LYS A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.953A pdb=" N GLN A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.530A pdb=" N ALA A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.988A pdb=" N ASP A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.592A pdb=" N ASP A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.638A pdb=" N ASN A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 429 through 438 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 504 through 507 removed outlier: 3.674A pdb=" N GLY A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.901A pdb=" N LYS A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.832A pdb=" N LYS F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.654A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.546A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.664A pdb=" N LEU B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.628A pdb=" N VAL B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 123 through 129 removed outlier: 4.070A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.835A pdb=" N LYS B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.953A pdb=" N GLN B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 154' Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.530A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.988A pdb=" N ASP B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.592A pdb=" N ASP B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.638A pdb=" N ASN B 362 " --> pdb=" O CYS B 358 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 429 through 438 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 504 through 507 removed outlier: 3.674A pdb=" N GLY B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 507' Processing helix chain 'B' and resid 508 through 514 removed outlier: 3.901A pdb=" N LYS B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.832A pdb=" N LYS D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.654A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.546A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU A 29 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 302 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 8.662A pdb=" N ILE A 216 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 172 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU A 218 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS A 220 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 176 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 215 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL A 240 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 217 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 239 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 275 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 267 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 390 Processing sheet with id=AA6, first strand: chain 'A' and resid 493 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 486 removed outlier: 4.123A pdb=" N LYS A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 547 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 18 through 24 removed outlier: 3.519A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.534A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.516A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.966A pdb=" N MET F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN F 59 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.691A pdb=" N SER I 25 " --> pdb=" O VAL I 2 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER I 57 " --> pdb=" O HIS I 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS I 52 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER I 57 " --> pdb=" O HIS I 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS I 52 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR I 94 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 5 through 6 removed outlier: 6.500A pdb=" N THR J 69 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.529A pdb=" N TYR J 49 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL J 34 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 89 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU B 29 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 302 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AC1, first strand: chain 'B' and resid 161 through 166 removed outlier: 8.662A pdb=" N ILE B 216 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 172 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 218 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 174 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS B 220 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR B 176 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 215 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL B 240 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA B 217 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 239 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 275 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 267 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AC3, first strand: chain 'B' and resid 387 through 390 Processing sheet with id=AC4, first strand: chain 'B' and resid 493 through 498 Processing sheet with id=AC5, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.123A pdb=" N LYS B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 547 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 18 through 24 removed outlier: 3.519A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.534A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.516A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.966A pdb=" N MET D 34 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 59 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 2 through 3 removed outlier: 3.691A pdb=" N SER G 25 " --> pdb=" O VAL G 2 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER G 57 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS G 52 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 56 through 60 removed outlier: 4.712A pdb=" N SER G 57 " --> pdb=" O HIS G 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS G 52 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 6 removed outlier: 6.500A pdb=" N THR H 69 " --> pdb=" O ALA H 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.529A pdb=" N TYR H 49 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 34 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 89 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3018 1.33 - 1.45: 4646 1.45 - 1.58: 7730 1.58 - 1.71: 0 1.71 - 1.84: 108 Bond restraints: 15502 Sorted by residual: bond pdb=" CA LYS G 74 " pdb=" C LYS G 74 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" CA LYS I 74 " pdb=" C LYS I 74 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" N TYR H 94 " pdb=" CA TYR H 94 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" N TYR J 94 " pdb=" CA TYR J 94 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.47e+01 bond pdb=" CA SER D 52 " pdb=" CB SER D 52 " ideal model delta sigma weight residual 1.527 1.472 0.054 1.44e-02 4.82e+03 1.43e+01 ... (remaining 15497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 20452 2.78 - 5.55: 506 5.55 - 8.33: 50 8.33 - 11.11: 8 11.11 - 13.88: 4 Bond angle restraints: 21020 Sorted by residual: angle pdb=" N CYS B 57 " pdb=" CA CYS B 57 " pdb=" C CYS B 57 " ideal model delta sigma weight residual 108.74 97.93 10.81 1.38e+00 5.25e-01 6.14e+01 angle pdb=" N CYS A 57 " pdb=" CA CYS A 57 " pdb=" C CYS A 57 " ideal model delta sigma weight residual 108.74 97.93 10.81 1.38e+00 5.25e-01 6.14e+01 angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 113.40 123.61 -10.21 1.47e+00 4.63e-01 4.82e+01 angle pdb=" N LYS B 97 " pdb=" CA LYS B 97 " pdb=" C LYS B 97 " ideal model delta sigma weight residual 113.40 123.61 -10.21 1.47e+00 4.63e-01 4.82e+01 angle pdb=" CA THR C 5 " pdb=" C THR C 5 " pdb=" O THR C 5 " ideal model delta sigma weight residual 120.81 112.87 7.94 1.15e+00 7.56e-01 4.77e+01 ... (remaining 21015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8034 17.89 - 35.79: 888 35.79 - 53.68: 196 53.68 - 71.58: 44 71.58 - 89.47: 20 Dihedral angle restraints: 9182 sinusoidal: 3608 harmonic: 5574 Sorted by residual: dihedral pdb=" CD ARG A 56 " pdb=" NE ARG A 56 " pdb=" CZ ARG A 56 " pdb=" NH1 ARG A 56 " ideal model delta sinusoidal sigma weight residual 0.00 -87.76 87.76 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG B 56 " pdb=" NE ARG B 56 " pdb=" CZ ARG B 56 " pdb=" NH1 ARG B 56 " ideal model delta sinusoidal sigma weight residual 0.00 -87.76 87.76 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG A 297 " pdb=" NE ARG A 297 " pdb=" CZ ARG A 297 " pdb=" NH1 ARG A 297 " ideal model delta sinusoidal sigma weight residual 0.00 -80.69 80.69 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 9179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2142 0.127 - 0.254: 120 0.254 - 0.380: 20 0.380 - 0.507: 0 0.507 - 0.634: 6 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA LYS A 97 " pdb=" N LYS A 97 " pdb=" C LYS A 97 " pdb=" CB LYS A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA LYS B 97 " pdb=" N LYS B 97 " pdb=" C LYS B 97 " pdb=" CB LYS B 97 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA THR B 90 " pdb=" N THR B 90 " pdb=" C THR B 90 " pdb=" CB THR B 90 " both_signs ideal model delta sigma weight residual False 2.53 1.91 0.62 2.00e-01 2.50e+01 9.49e+00 ... (remaining 2285 not shown) Planarity restraints: 2698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 56 " 1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 56 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 56 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 56 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 56 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 56 " 1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 56 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 56 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 56 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 56 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 297 " -1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A 297 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 297 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 297 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 297 " -0.019 2.00e-02 2.50e+03 ... (remaining 2695 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 254 2.63 - 3.20: 13208 3.20 - 3.76: 20476 3.76 - 4.33: 30880 4.33 - 4.90: 53331 Nonbonded interactions: 118149 Sorted by model distance: nonbonded pdb=" OD1 ASP G 109 " pdb=" N VAL G 110 " model vdw 2.059 3.120 nonbonded pdb=" OD1 ASP I 109 " pdb=" N VAL I 110 " model vdw 2.059 3.120 nonbonded pdb=" O ASN I 54 " pdb=" OG SER I 55 " model vdw 2.062 3.040 nonbonded pdb=" O ASN G 54 " pdb=" OG SER G 55 " model vdw 2.062 3.040 nonbonded pdb=" OD2 ASP B 85 " pdb="ZN ZN B 601 " model vdw 2.068 2.230 ... (remaining 118144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.800 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.890 ------------------------------------------------------------------------------- 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 15524 Z= 0.490 Angle : 1.039 13.882 21052 Z= 0.660 Chirality : 0.077 0.634 2288 Planarity : 0.027 0.494 2698 Dihedral : 16.228 89.470 5602 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.97 % Allowed : 4.74 % Favored : 94.28 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.17), residues: 1924 helix: -1.62 (0.28), residues: 266 sheet: -1.49 (0.22), residues: 586 loop : -2.84 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 401 TYR 0.047 0.005 TYR J 94 PHE 0.020 0.004 PHE A 183 TRP 0.024 0.003 TRP D 47 HIS 0.007 0.002 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00798 (15502) covalent geometry : angle 1.03440 (21020) SS BOND : bond 0.02384 ( 16) SS BOND : angle 2.58834 ( 32) hydrogen bonds : bond 0.23461 ( 410) hydrogen bonds : angle 9.18213 ( 1152) metal coordination : bond 0.27287 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.647 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: 0.1347 time to fit residues: 46.3105 Evaluate side-chains 210 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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 = 0.3835 r_free = 0.3835 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115854 restraints weight = 19554.359| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.32 r_work: 0.3303 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15524 Z= 0.142 Angle : 0.703 11.820 21052 Z= 0.368 Chirality : 0.050 0.261 2288 Planarity : 0.005 0.093 2698 Dihedral : 5.726 54.787 2130 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.70 % Allowed : 10.34 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.18), residues: 1924 helix: -0.56 (0.29), residues: 290 sheet: -0.88 (0.22), residues: 590 loop : -2.47 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 354 TYR 0.022 0.002 TYR C 91 PHE 0.019 0.002 PHE J 71 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00329 (15502) covalent geometry : angle 0.69311 (21020) SS BOND : bond 0.00538 ( 16) SS BOND : angle 3.10229 ( 32) hydrogen bonds : bond 0.04746 ( 410) hydrogen bonds : angle 5.88413 ( 1152) metal coordination : bond 0.00414 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7286 (mm-30) REVERT: A 330 LYS cc_start: 0.7861 (mttm) cc_final: 0.7486 (mtpp) REVERT: I 105 GLU cc_start: 0.7710 (mp0) cc_final: 0.7424 (mp0) REVERT: J 20 THR cc_start: 0.6795 (p) cc_final: 0.6305 (m) REVERT: B 134 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7283 (mm-30) REVERT: B 330 LYS cc_start: 0.7858 (mttm) cc_final: 0.7486 (mtpp) REVERT: G 105 GLU cc_start: 0.7704 (mp0) cc_final: 0.7413 (mp0) REVERT: H 20 THR cc_start: 0.6825 (p) cc_final: 0.6333 (m) outliers start: 28 outliers final: 22 residues processed: 230 average time/residue: 0.1376 time to fit residues: 46.5149 Evaluate side-chains 220 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 57 optimal weight: 0.0060 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118333 restraints weight = 20115.551| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.44 r_work: 0.3335 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15524 Z= 0.102 Angle : 0.584 7.132 21052 Z= 0.307 Chirality : 0.046 0.175 2288 Planarity : 0.005 0.086 2698 Dihedral : 5.365 56.405 2130 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.97 % Allowed : 14.11 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.19), residues: 1924 helix: 0.18 (0.31), residues: 282 sheet: -0.55 (0.23), residues: 574 loop : -2.15 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 87 TYR 0.015 0.001 TYR E 91 PHE 0.021 0.001 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.003 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00228 (15502) covalent geometry : angle 0.57988 (21020) SS BOND : bond 0.00374 ( 16) SS BOND : angle 1.94345 ( 32) hydrogen bonds : bond 0.03483 ( 410) hydrogen bonds : angle 5.16636 ( 1152) metal coordination : bond 0.00042 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7360 (mm-30) REVERT: A 379 MET cc_start: 0.8482 (tmm) cc_final: 0.8140 (tmm) REVERT: I 20 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7124 (mt) REVERT: I 100 TYR cc_start: 0.7938 (t80) cc_final: 0.7694 (t80) REVERT: J 20 THR cc_start: 0.6846 (p) cc_final: 0.6368 (m) REVERT: B 134 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7354 (mm-30) REVERT: B 379 MET cc_start: 0.8483 (tmm) cc_final: 0.8138 (tmm) REVERT: G 20 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7133 (mt) REVERT: G 100 TYR cc_start: 0.7942 (t80) cc_final: 0.7697 (t80) REVERT: H 20 THR cc_start: 0.6857 (p) cc_final: 0.6381 (m) outliers start: 16 outliers final: 12 residues processed: 218 average time/residue: 0.1371 time to fit residues: 44.1277 Evaluate side-chains 216 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain I residue 20 LEU 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 87 TYR Chi-restraints excluded: chain C residue 5 THR 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 H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 146 optimal weight: 0.0040 overall best weight: 0.7614 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114009 restraints weight = 20122.415| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.37 r_work: 0.3281 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15524 Z= 0.125 Angle : 0.597 7.176 21052 Z= 0.312 Chirality : 0.047 0.192 2288 Planarity : 0.004 0.084 2698 Dihedral : 5.399 56.565 2130 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.89 % Allowed : 15.39 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.19), residues: 1924 helix: 0.05 (0.31), residues: 298 sheet: -0.34 (0.23), residues: 566 loop : -2.04 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 87 TYR 0.021 0.002 TYR C 91 PHE 0.020 0.001 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00300 (15502) covalent geometry : angle 0.59162 (21020) SS BOND : bond 0.00419 ( 16) SS BOND : angle 2.22051 ( 32) hydrogen bonds : bond 0.03911 ( 410) hydrogen bonds : angle 4.89186 ( 1152) metal coordination : bond 0.00210 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.842 Fit side-chains REVERT: A 134 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7398 (mm-30) REVERT: A 330 LYS cc_start: 0.7887 (mttm) cc_final: 0.7538 (mtpp) REVERT: A 402 ASN cc_start: 0.8344 (t0) cc_final: 0.8115 (t0) REVERT: J 20 THR cc_start: 0.6886 (p) cc_final: 0.6614 (m) REVERT: J 90 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7539 (pp30) REVERT: J 94 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6238 (t80) REVERT: B 134 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7386 (mm-30) REVERT: B 330 LYS cc_start: 0.7895 (mttm) cc_final: 0.7549 (mtpp) REVERT: B 402 ASN cc_start: 0.8347 (t0) cc_final: 0.8118 (t0) REVERT: H 20 THR cc_start: 0.6898 (p) cc_final: 0.6623 (m) REVERT: H 90 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7540 (pp30) REVERT: H 94 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6238 (t80) outliers start: 31 outliers final: 22 residues processed: 222 average time/residue: 0.1351 time to fit residues: 44.6393 Evaluate side-chains 230 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain F residue 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 89 LEU Chi-restraints excluded: chain J residue 90 GLN Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 125 optimal weight: 0.0170 chunk 165 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113248 restraints weight = 20129.912| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.46 r_work: 0.3263 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15524 Z= 0.128 Angle : 0.594 7.329 21052 Z= 0.309 Chirality : 0.047 0.194 2288 Planarity : 0.005 0.093 2698 Dihedral : 5.409 56.296 2130 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.62 % Allowed : 16.12 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1924 helix: 0.15 (0.31), residues: 296 sheet: -0.20 (0.23), residues: 580 loop : -2.00 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.020 0.001 TYR C 91 PHE 0.019 0.001 PHE B 380 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00310 (15502) covalent geometry : angle 0.58905 (21020) SS BOND : bond 0.00394 ( 16) SS BOND : angle 2.00491 ( 32) hydrogen bonds : bond 0.03740 ( 410) hydrogen bonds : angle 4.74351 ( 1152) metal coordination : bond 0.00237 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.633 Fit side-chains REVERT: A 113 MET cc_start: 0.8642 (ttt) cc_final: 0.8263 (ttt) REVERT: A 134 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 330 LYS cc_start: 0.7848 (mttm) cc_final: 0.7525 (mtpp) REVERT: A 402 ASN cc_start: 0.8323 (t0) cc_final: 0.8075 (t0) REVERT: F 89 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7176 (mp0) REVERT: I 20 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7210 (mt) REVERT: J 20 THR cc_start: 0.7026 (p) cc_final: 0.6566 (m) REVERT: J 94 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6591 (t80) REVERT: J 103 LYS cc_start: 0.6640 (mtmt) cc_final: 0.6273 (mttt) REVERT: B 113 MET cc_start: 0.8657 (ttt) cc_final: 0.8283 (ttt) REVERT: B 134 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7273 (mp0) REVERT: B 330 LYS cc_start: 0.7856 (mttm) cc_final: 0.7532 (mtpp) REVERT: B 402 ASN cc_start: 0.8329 (t0) cc_final: 0.8080 (t0) REVERT: D 89 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7160 (mp0) REVERT: G 20 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7206 (mt) REVERT: H 20 THR cc_start: 0.7038 (p) cc_final: 0.6574 (m) REVERT: H 94 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6600 (t80) REVERT: H 103 LYS cc_start: 0.6631 (mtmt) cc_final: 0.6261 (mttt) outliers start: 43 outliers final: 27 residues processed: 228 average time/residue: 0.1334 time to fit residues: 45.2797 Evaluate side-chains 225 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain 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 15 VAL Chi-restraints excluded: chain J 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 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113576 restraints weight = 20260.118| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.47 r_work: 0.3267 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15524 Z= 0.113 Angle : 0.578 6.857 21052 Z= 0.303 Chirality : 0.047 0.263 2288 Planarity : 0.004 0.085 2698 Dihedral : 5.327 56.173 2130 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.04 % Allowed : 16.91 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.19), residues: 1924 helix: 0.31 (0.31), residues: 296 sheet: -0.20 (0.23), residues: 566 loop : -1.87 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.016 0.001 TYR E 91 PHE 0.022 0.001 PHE A 380 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00269 (15502) covalent geometry : angle 0.57335 (21020) SS BOND : bond 0.00345 ( 16) SS BOND : angle 1.88881 ( 32) hydrogen bonds : bond 0.03424 ( 410) hydrogen bonds : angle 4.62503 ( 1152) metal coordination : bond 0.00187 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.734 Fit side-chains REVERT: A 113 MET cc_start: 0.8627 (ttt) cc_final: 0.8220 (ttt) REVERT: A 134 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 250 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8581 (t) REVERT: A 274 LYS cc_start: 0.6672 (mmtp) cc_final: 0.6466 (mmtp) REVERT: A 330 LYS cc_start: 0.7826 (mttm) cc_final: 0.7509 (mtpp) REVERT: A 379 MET cc_start: 0.8461 (tmm) cc_final: 0.7934 (tmm) REVERT: A 402 ASN cc_start: 0.8322 (t0) cc_final: 0.8090 (t0) REVERT: E 11 LEU cc_start: 0.7296 (mt) cc_final: 0.6842 (pp) REVERT: E 94 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.6264 (t80) REVERT: F 89 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7229 (mp0) REVERT: I 20 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7190 (mt) REVERT: I 50 MET cc_start: 0.8358 (ptp) cc_final: 0.8133 (ptp) REVERT: J 20 THR cc_start: 0.6955 (p) cc_final: 0.6687 (m) REVERT: J 88 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6863 (p) REVERT: J 94 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6445 (t80) REVERT: J 103 LYS cc_start: 0.6550 (mtmt) cc_final: 0.6177 (mttt) REVERT: B 113 MET cc_start: 0.8646 (ttt) cc_final: 0.8246 (ttt) REVERT: B 134 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7445 (mm-30) REVERT: B 250 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8578 (t) REVERT: B 330 LYS cc_start: 0.7826 (mttm) cc_final: 0.7507 (mtpp) REVERT: B 379 MET cc_start: 0.8433 (tmm) cc_final: 0.7910 (tmm) REVERT: B 402 ASN cc_start: 0.8325 (t0) cc_final: 0.8090 (t0) REVERT: C 11 LEU cc_start: 0.7296 (mt) cc_final: 0.6848 (pp) REVERT: C 94 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.6276 (t80) REVERT: D 89 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7219 (mp0) REVERT: G 20 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7189 (mt) REVERT: G 50 MET cc_start: 0.8357 (ptp) cc_final: 0.8129 (ptp) REVERT: H 20 THR cc_start: 0.6961 (p) cc_final: 0.6692 (m) REVERT: H 88 CYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6887 (p) REVERT: H 94 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6452 (t80) REVERT: H 103 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6179 (mttt) outliers start: 50 outliers final: 34 residues processed: 226 average time/residue: 0.1316 time to fit residues: 44.0051 Evaluate side-chains 236 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 250 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 THR 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 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 213 ASN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 58 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 69 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 22 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 111 optimal weight: 0.0040 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 167 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5850 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113796 restraints weight = 20083.283| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.47 r_work: 0.3272 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15524 Z= 0.112 Angle : 0.570 6.892 21052 Z= 0.298 Chirality : 0.046 0.198 2288 Planarity : 0.004 0.078 2698 Dihedral : 5.248 55.820 2130 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.98 % Allowed : 17.15 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.19), residues: 1924 helix: 0.42 (0.31), residues: 296 sheet: -0.10 (0.23), residues: 566 loop : -1.84 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.016 0.001 TYR E 91 PHE 0.022 0.001 PHE B 380 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00266 (15502) covalent geometry : angle 0.56598 (21020) SS BOND : bond 0.00338 ( 16) SS BOND : angle 1.90910 ( 32) hydrogen bonds : bond 0.03357 ( 410) hydrogen bonds : angle 4.55429 ( 1152) metal coordination : bond 0.00177 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8066 (mp0) cc_final: 0.7483 (tt0) REVERT: A 113 MET cc_start: 0.8647 (ttt) cc_final: 0.8237 (ttt) REVERT: A 250 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 330 LYS cc_start: 0.7777 (mttm) cc_final: 0.7471 (mtpp) REVERT: A 379 MET cc_start: 0.8457 (tmm) cc_final: 0.7960 (tmm) REVERT: A 402 ASN cc_start: 0.8324 (t0) cc_final: 0.8118 (t0) REVERT: A 497 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8360 (pp) REVERT: E 11 LEU cc_start: 0.7281 (mt) cc_final: 0.6829 (pp) REVERT: E 94 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6304 (t80) REVERT: F 89 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7224 (mp0) REVERT: I 20 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7114 (mt) REVERT: J 20 THR cc_start: 0.6941 (p) cc_final: 0.6640 (m) REVERT: J 88 CYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6818 (p) REVERT: J 94 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6313 (t80) REVERT: J 103 LYS cc_start: 0.6455 (mtmt) cc_final: 0.6136 (mttt) REVERT: B 46 GLU cc_start: 0.8070 (mp0) cc_final: 0.7480 (tt0) REVERT: B 113 MET cc_start: 0.8660 (ttt) cc_final: 0.8254 (ttt) REVERT: B 250 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (t) REVERT: B 330 LYS cc_start: 0.7785 (mttm) cc_final: 0.7479 (mtpp) REVERT: B 379 MET cc_start: 0.8426 (tmm) cc_final: 0.7927 (tmm) REVERT: B 402 ASN cc_start: 0.8329 (t0) cc_final: 0.8119 (t0) REVERT: B 497 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8359 (pp) REVERT: C 11 LEU cc_start: 0.7278 (mt) cc_final: 0.6833 (pp) REVERT: C 94 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.6311 (t80) REVERT: D 89 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7208 (mp0) REVERT: G 20 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7110 (mt) REVERT: H 20 THR cc_start: 0.6952 (p) cc_final: 0.6647 (m) REVERT: H 88 CYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6835 (p) REVERT: H 94 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6322 (t80) REVERT: H 103 LYS cc_start: 0.6467 (mtmt) cc_final: 0.6145 (mttt) outliers start: 49 outliers final: 33 residues processed: 228 average time/residue: 0.1330 time to fit residues: 45.2575 Evaluate side-chains 237 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 250 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 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 15 VAL Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 122 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114425 restraints weight = 20271.397| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.49 r_work: 0.3281 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15524 Z= 0.104 Angle : 0.559 6.666 21052 Z= 0.292 Chirality : 0.046 0.242 2288 Planarity : 0.004 0.076 2698 Dihedral : 5.132 55.816 2130 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.80 % Allowed : 17.64 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.19), residues: 1924 helix: 0.55 (0.32), residues: 296 sheet: -0.09 (0.23), residues: 568 loop : -1.80 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.015 0.001 TYR E 91 PHE 0.023 0.001 PHE A 380 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00245 (15502) covalent geometry : angle 0.55470 (21020) SS BOND : bond 0.00284 ( 16) SS BOND : angle 1.79596 ( 32) hydrogen bonds : bond 0.03170 ( 410) hydrogen bonds : angle 4.47907 ( 1152) metal coordination : bond 0.00148 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.638 Fit side-chains REVERT: A 46 GLU cc_start: 0.8070 (mp0) cc_final: 0.7504 (tt0) REVERT: A 113 MET cc_start: 0.8646 (ttt) cc_final: 0.8236 (ttt) REVERT: A 134 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 312 SER cc_start: 0.8141 (t) cc_final: 0.7869 (p) REVERT: A 330 LYS cc_start: 0.7769 (mttm) cc_final: 0.7444 (mtpp) REVERT: A 379 MET cc_start: 0.8465 (tmm) cc_final: 0.7987 (tmm) REVERT: A 489 MET cc_start: 0.8637 (mmt) cc_final: 0.8251 (mmt) REVERT: A 497 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8335 (pp) REVERT: E 11 LEU cc_start: 0.7252 (mt) cc_final: 0.6813 (pp) REVERT: E 94 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6224 (t80) REVERT: F 89 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7237 (mp0) REVERT: I 20 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7113 (mt) REVERT: I 50 MET cc_start: 0.8222 (ptp) cc_final: 0.7955 (ptm) REVERT: J 20 THR cc_start: 0.6937 (p) cc_final: 0.6685 (m) REVERT: J 88 CYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6803 (p) REVERT: J 103 LYS cc_start: 0.6540 (mtmt) cc_final: 0.6223 (mttt) REVERT: B 46 GLU cc_start: 0.8072 (mp0) cc_final: 0.7496 (tt0) REVERT: B 113 MET cc_start: 0.8658 (ttt) cc_final: 0.8251 (ttt) REVERT: B 134 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7487 (mt-10) REVERT: B 312 SER cc_start: 0.8146 (t) cc_final: 0.7873 (p) REVERT: B 330 LYS cc_start: 0.7776 (mttm) cc_final: 0.7450 (mtpp) REVERT: B 379 MET cc_start: 0.8458 (tmm) cc_final: 0.7981 (tmm) REVERT: B 489 MET cc_start: 0.8634 (mmt) cc_final: 0.8246 (mmt) REVERT: B 497 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8333 (pp) REVERT: C 11 LEU cc_start: 0.7250 (mt) cc_final: 0.6816 (pp) REVERT: C 94 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6235 (t80) REVERT: D 89 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7231 (mp0) REVERT: G 20 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7108 (mt) REVERT: G 50 MET cc_start: 0.8219 (ptp) cc_final: 0.7947 (ptm) REVERT: H 20 THR cc_start: 0.6941 (p) cc_final: 0.6689 (m) REVERT: H 88 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6811 (p) REVERT: H 103 LYS cc_start: 0.6543 (mtmt) cc_final: 0.6226 (mttt) outliers start: 46 outliers final: 36 residues processed: 234 average time/residue: 0.1322 time to fit residues: 45.9152 Evaluate side-chains 242 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 THR 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 88 CYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain B residue 87 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 58 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 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 138 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 189 optimal weight: 0.0670 chunk 74 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 161 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.148643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115743 restraints weight = 19874.091| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.38 r_work: 0.3290 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15524 Z= 0.105 Angle : 0.566 7.000 21052 Z= 0.297 Chirality : 0.046 0.214 2288 Planarity : 0.004 0.074 2698 Dihedral : 5.123 55.871 2130 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.04 % Allowed : 17.52 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.19), residues: 1924 helix: 0.60 (0.32), residues: 296 sheet: 0.01 (0.23), residues: 556 loop : -1.80 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.014 0.001 TYR C 91 PHE 0.025 0.001 PHE A 380 TRP 0.011 0.001 TRP D 47 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00248 (15502) covalent geometry : angle 0.56174 (21020) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.82383 ( 32) hydrogen bonds : bond 0.03150 ( 410) hydrogen bonds : angle 4.46472 ( 1152) metal coordination : bond 0.00138 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8018 (mp0) cc_final: 0.7483 (tt0) REVERT: A 113 MET cc_start: 0.8629 (ttt) cc_final: 0.8210 (ttt) REVERT: A 312 SER cc_start: 0.8139 (t) cc_final: 0.7865 (p) REVERT: A 330 LYS cc_start: 0.7760 (mttm) cc_final: 0.7439 (mtpp) REVERT: A 379 MET cc_start: 0.8456 (tmm) cc_final: 0.8038 (tmm) REVERT: A 489 MET cc_start: 0.8592 (mmt) cc_final: 0.8205 (mmt) REVERT: A 497 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8322 (pp) REVERT: E 11 LEU cc_start: 0.7245 (mt) cc_final: 0.6824 (pp) REVERT: E 94 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.6197 (t80) REVERT: F 89 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7219 (mp0) REVERT: I 20 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7118 (mt) REVERT: I 50 MET cc_start: 0.8268 (ptp) cc_final: 0.8012 (ptm) REVERT: J 20 THR cc_start: 0.6957 (p) cc_final: 0.6722 (m) REVERT: J 88 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6782 (p) REVERT: J 103 LYS cc_start: 0.6584 (mtmt) cc_final: 0.6258 (mttt) REVERT: B 46 GLU cc_start: 0.8033 (mp0) cc_final: 0.7479 (tt0) REVERT: B 113 MET cc_start: 0.8641 (ttt) cc_final: 0.8226 (ttt) REVERT: B 312 SER cc_start: 0.8146 (t) cc_final: 0.7870 (p) REVERT: B 330 LYS cc_start: 0.7773 (mttm) cc_final: 0.7451 (mtpp) REVERT: B 379 MET cc_start: 0.8455 (tmm) cc_final: 0.8037 (tmm) REVERT: B 489 MET cc_start: 0.8585 (mmt) cc_final: 0.8198 (mmt) REVERT: B 497 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8321 (pp) REVERT: C 11 LEU cc_start: 0.7243 (mt) cc_final: 0.6827 (pp) REVERT: C 94 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.6207 (t80) REVERT: D 89 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7206 (mp0) REVERT: G 20 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7110 (mt) REVERT: G 50 MET cc_start: 0.8264 (ptp) cc_final: 0.8004 (ptm) REVERT: H 20 THR cc_start: 0.6952 (p) cc_final: 0.6715 (m) REVERT: H 88 CYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6789 (p) REVERT: H 103 LYS cc_start: 0.6579 (mtmt) cc_final: 0.6255 (mttt) outliers start: 50 outliers final: 39 residues processed: 236 average time/residue: 0.1324 time to fit residues: 46.5374 Evaluate side-chains 246 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 THR 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 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 58 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 15 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 90 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112473 restraints weight = 20178.923| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.46 r_work: 0.3268 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15524 Z= 0.124 Angle : 0.594 7.227 21052 Z= 0.310 Chirality : 0.047 0.244 2288 Planarity : 0.004 0.077 2698 Dihedral : 5.193 55.619 2130 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.98 % Allowed : 18.07 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.19), residues: 1924 helix: 0.48 (0.31), residues: 296 sheet: 0.01 (0.23), residues: 562 loop : -1.80 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.020 0.001 TYR C 91 PHE 0.024 0.001 PHE B 380 TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00297 (15502) covalent geometry : angle 0.58875 (21020) SS BOND : bond 0.00399 ( 16) SS BOND : angle 2.01254 ( 32) hydrogen bonds : bond 0.03483 ( 410) hydrogen bonds : angle 4.50037 ( 1152) metal coordination : bond 0.00222 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7997 (mp0) cc_final: 0.7466 (tt0) REVERT: A 113 MET cc_start: 0.8681 (ttt) cc_final: 0.8282 (ttt) REVERT: A 312 SER cc_start: 0.8139 (t) cc_final: 0.7870 (p) REVERT: A 330 LYS cc_start: 0.7764 (mttm) cc_final: 0.7458 (mtpp) REVERT: A 379 MET cc_start: 0.8493 (tmm) cc_final: 0.8104 (tmm) REVERT: A 489 MET cc_start: 0.8564 (mmt) cc_final: 0.8104 (mmt) REVERT: A 497 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8348 (pp) REVERT: E 11 LEU cc_start: 0.7263 (mt) cc_final: 0.6828 (pp) REVERT: E 94 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.6250 (t80) REVERT: F 43 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7642 (mttp) REVERT: F 89 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7236 (mp0) REVERT: I 50 MET cc_start: 0.8316 (ptp) cc_final: 0.8071 (ptm) REVERT: J 20 THR cc_start: 0.7000 (p) cc_final: 0.6744 (m) REVERT: J 88 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6818 (p) REVERT: J 103 LYS cc_start: 0.6660 (mtmt) cc_final: 0.6324 (mttt) REVERT: B 46 GLU cc_start: 0.8014 (mp0) cc_final: 0.7467 (tt0) REVERT: B 113 MET cc_start: 0.8679 (ttt) cc_final: 0.8284 (ttt) REVERT: B 312 SER cc_start: 0.8140 (t) cc_final: 0.7871 (p) REVERT: B 330 LYS cc_start: 0.7767 (mttm) cc_final: 0.7460 (mtpp) REVERT: B 379 MET cc_start: 0.8486 (tmm) cc_final: 0.8092 (tmm) REVERT: B 489 MET cc_start: 0.8565 (mmt) cc_final: 0.8105 (mmt) REVERT: B 497 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 11 LEU cc_start: 0.7260 (mt) cc_final: 0.6829 (pp) REVERT: C 94 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.6262 (t80) REVERT: D 43 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7643 (mttp) REVERT: D 89 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7237 (mp0) REVERT: G 50 MET cc_start: 0.8308 (ptp) cc_final: 0.8056 (ptm) REVERT: H 20 THR cc_start: 0.7003 (p) cc_final: 0.6747 (m) REVERT: H 88 CYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6801 (p) REVERT: H 103 LYS cc_start: 0.6672 (mtmt) cc_final: 0.6334 (mttt) outliers start: 49 outliers final: 41 residues processed: 228 average time/residue: 0.1339 time to fit residues: 45.2531 Evaluate side-chains 237 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 91 TYR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 58 THR 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 213 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 58 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 15 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110603 restraints weight = 20198.794| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.48 r_work: 0.3222 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15524 Z= 0.181 Angle : 0.658 7.687 21052 Z= 0.344 Chirality : 0.049 0.208 2288 Planarity : 0.005 0.080 2698 Dihedral : 5.521 54.392 2130 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.92 % Allowed : 18.00 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.19), residues: 1924 helix: 0.28 (0.31), residues: 292 sheet: 0.03 (0.23), residues: 588 loop : -1.95 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.027 0.002 TYR E 94 PHE 0.025 0.002 PHE A 380 TRP 0.010 0.001 TRP F 47 HIS 0.005 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00451 (15502) covalent geometry : angle 0.65229 (21020) SS BOND : bond 0.00400 ( 16) SS BOND : angle 2.38658 ( 32) hydrogen bonds : bond 0.04392 ( 410) hydrogen bonds : angle 4.72786 ( 1152) metal coordination : bond 0.00411 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4859.87 seconds wall clock time: 83 minutes 55.24 seconds (5035.24 seconds total)