Starting phenix.real_space_refine on Mon May 19 19:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5k_42983/05_2025/8v5k_42983.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4551 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 9654 2.51 5 N 2655 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15336 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "G" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "C" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3256 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 14, 'TRANS': 404} Chain breaks: 5 Chain: "E" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "F" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "I" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.38, per 1000 atoms: 0.61 Number of scatterers: 15336 At special positions: 0 Unit cell: (134.42, 134.42, 125.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2958 8.00 N 2655 7.00 C 9654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.04 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 104 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 359 " " NAG B 601 " - " ASN B 359 " " NAG C 601 " - " ASN C 359 " Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 33 sheets defined 29.6% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 64 through 91 removed outlier: 4.155A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 125 through 154 removed outlier: 4.677A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 191 removed outlier: 4.062A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.998A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.553A pdb=" N ILE A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'D' and resid 26 through 29 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.837A pdb=" N THR G 99 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 64 through 91 removed outlier: 4.167A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 125 through 154 removed outlier: 4.712A pdb=" N GLN B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 4.032A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.127A pdb=" N LEU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.738A pdb=" N ILE B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.553A pdb=" N ILE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 64 through 91 removed outlier: 4.163A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 125 through 137 Processing helix chain 'C' and resid 137 through 154 removed outlier: 3.628A pdb=" N SER C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 191 removed outlier: 4.014A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.982A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.756A pdb=" N ILE C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 481 Processing helix chain 'E' and resid 27 through 30 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 112A through 113 No H-bonds generated for 'chain 'E' and resid 112A through 113' Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 112A through 113 No H-bonds generated for 'chain 'F' and resid 112A through 113' Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.851A pdb=" N THR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.832A pdb=" N THR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.778A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS A 263 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG A 281 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 269 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 293 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY A 37 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR A 291 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.849A pdb=" N THR A 117 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A 114 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN C 428 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY A 116 " --> pdb=" O ASN C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 removed outlier: 6.854A pdb=" N LEU A 426 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 116 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B 117 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.370A pdb=" N VAL D 12 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG D 40 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.370A pdb=" N VAL D 12 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS D 98 " --> pdb=" O TRP D 114 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TRP D 114 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 100 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 2 through 7 removed outlier: 3.605A pdb=" N THR G 77 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 8.108A pdb=" N LYS G 37 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR G 57 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU G 39 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP G 41 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AB6, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.360A pdb=" N THR B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 269 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 293 " --> pdb=" O PRO B 35 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 37 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N THR B 291 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 394 removed outlier: 8.177A pdb=" N LEU B 426 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR C 117 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN B 428 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 117 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.400A pdb=" N THR C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 269 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 43 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR C 286 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C 41 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 293 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY C 37 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR C 291 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.336A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG E 43 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N PHE E 52 " --> pdb=" O ARG E 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 12 through 14 removed outlier: 6.336A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS E 104 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TRP E 118 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 106 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.339A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG F 43 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 12 through 14 removed outlier: 6.339A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS F 104 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TRP F 118 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL F 106 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 2 through 7 removed outlier: 3.566A pdb=" N THR H 77 " --> pdb=" O ARG H 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 13 removed outlier: 8.159A pdb=" N LYS H 37 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 57 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 39 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AD4, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.587A pdb=" N THR I 77 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 13 removed outlier: 8.073A pdb=" N LYS I 37 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR I 57 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU I 39 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 11 through 13 787 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5085 1.34 - 1.46: 2686 1.46 - 1.58: 7709 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 15570 Sorted by residual: bond pdb=" CB THR A 393 " pdb=" CG2 THR A 393 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.13e+00 bond pdb=" CB THR B 393 " pdb=" CG2 THR B 393 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.49e+00 bond pdb=" CB THR C 393 " pdb=" CG2 THR C 393 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 15565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 20568 2.11 - 4.21: 460 4.21 - 6.32: 50 6.32 - 8.43: 4 8.43 - 10.54: 2 Bond angle restraints: 21084 Sorted by residual: angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.02 115.74 -4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.02 115.59 -4.57 1.22e+00 6.72e-01 1.40e+01 angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.02 115.55 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CA LEU B 78 " pdb=" CB LEU B 78 " pdb=" CG LEU B 78 " ideal model delta sigma weight residual 116.30 126.84 -10.54 3.50e+00 8.16e-02 9.06e+00 angle pdb=" N CYS A 394 " pdb=" CA CYS A 394 " pdb=" C CYS A 394 " ideal model delta sigma weight residual 108.90 113.51 -4.61 1.63e+00 3.76e-01 8.01e+00 ... (remaining 21079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 8954 17.50 - 35.00: 449 35.00 - 52.49: 69 52.49 - 69.99: 21 69.99 - 87.49: 23 Dihedral angle restraints: 9516 sinusoidal: 3831 harmonic: 5685 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -134.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -132.96 46.96 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -130.65 44.65 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1450 0.040 - 0.079: 677 0.079 - 0.119: 264 0.119 - 0.158: 57 0.158 - 0.198: 12 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA LEU G 114 " pdb=" N LEU G 114 " pdb=" C LEU G 114 " pdb=" CB LEU G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CG LEU G 4 " pdb=" CB LEU G 4 " pdb=" CD1 LEU G 4 " pdb=" CD2 LEU G 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA LEU I 114 " pdb=" N LEU I 114 " pdb=" C LEU I 114 " pdb=" CB LEU I 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2457 not shown) Planarity restraints: 2703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 281 " -0.316 9.50e-02 1.11e+02 1.45e-01 2.39e+01 pdb=" NE ARG B 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG B 281 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B 281 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 281 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 281 " 0.279 9.50e-02 1.11e+02 1.28e-01 1.77e+01 pdb=" NE ARG A 281 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG A 281 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 281 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 281 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 281 " 0.226 9.50e-02 1.11e+02 1.04e-01 1.20e+01 pdb=" NE ARG C 281 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG C 281 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG C 281 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 281 " 0.022 2.00e-02 2.50e+03 ... (remaining 2700 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1756 2.75 - 3.29: 14538 3.29 - 3.83: 24006 3.83 - 4.36: 29604 4.36 - 4.90: 51468 Nonbonded interactions: 121372 Sorted by model distance: nonbonded pdb=" OG SER G 55 " pdb=" OD1 ASN G 66 " model vdw 2.217 3.040 nonbonded pdb=" OG SER H 55 " pdb=" OD1 ASN H 66 " model vdw 2.236 3.040 nonbonded pdb=" OG SER G 7 " pdb=" OG SER G 22 " model vdw 2.242 3.040 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.263 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 22 " model vdw 2.264 3.040 ... (remaining 121367 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: 0.10 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.007 0.088 15597 Z= 0.269 Angle : 0.753 10.536 21141 Z= 0.423 Chirality : 0.052 0.198 2460 Planarity : 0.006 0.145 2700 Dihedral : 11.790 87.490 5796 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1932 helix: 0.07 (0.23), residues: 423 sheet: 0.62 (0.20), residues: 580 loop : 0.80 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 473 HIS 0.008 0.002 HIS D 30 PHE 0.027 0.003 PHE C 111 TYR 0.044 0.004 TYR I 117 ARG 0.059 0.002 ARG B 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 1.77805 ( 9) hydrogen bonds : bond 0.21618 ( 754) hydrogen bonds : angle 7.77288 ( 2079) SS BOND : bond 0.00375 ( 24) SS BOND : angle 0.89682 ( 48) covalent geometry : bond 0.00685 (15570) covalent geometry : angle 0.75159 (21084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.7555 (mm110) cc_final: 0.7303 (mm110) REVERT: A 136 GLU cc_start: 0.7401 (tt0) cc_final: 0.6986 (tt0) REVERT: A 181 LYS cc_start: 0.7978 (mttm) cc_final: 0.7622 (mttm) REVERT: A 193 GLU cc_start: 0.7194 (tt0) cc_final: 0.6939 (tt0) REVERT: A 261 SER cc_start: 0.8048 (t) cc_final: 0.7723 (p) REVERT: A 349 ASN cc_start: 0.7371 (t0) cc_final: 0.7024 (t0) REVERT: A 351 GLU cc_start: 0.7564 (mp0) cc_final: 0.6919 (mp0) REVERT: A 466 ASP cc_start: 0.7629 (m-30) cc_final: 0.7325 (m-30) REVERT: G 117 TYR cc_start: 0.8303 (m-10) cc_final: 0.7873 (m-80) REVERT: B 21 ASP cc_start: 0.7891 (t70) cc_final: 0.7622 (t0) REVERT: B 38 MET cc_start: 0.7640 (ttp) cc_final: 0.7433 (ttm) REVERT: B 66 GLN cc_start: 0.7439 (tp-100) cc_final: 0.7144 (tp-100) REVERT: B 189 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6186 (ttp-110) REVERT: B 287 ARG cc_start: 0.7196 (ttt-90) cc_final: 0.6931 (ttt-90) REVERT: B 362 GLN cc_start: 0.8466 (mm110) cc_final: 0.8085 (mm110) REVERT: B 406 ASP cc_start: 0.7891 (p0) cc_final: 0.7670 (p0) REVERT: B 462 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7439 (ttmm) REVERT: B 466 ASP cc_start: 0.7520 (m-30) cc_final: 0.7259 (m-30) REVERT: B 468 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7030 (mm-30) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 1.4634 time to fit residues: 596.0382 Evaluate side-chains 312 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.0470 chunk 145 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 304 GLN B 418 ASN C 290 ASN C 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111871 restraints weight = 20289.469| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.00 r_work: 0.3304 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15597 Z= 0.148 Angle : 0.611 10.261 21141 Z= 0.327 Chirality : 0.046 0.175 2460 Planarity : 0.004 0.034 2700 Dihedral : 5.142 32.751 2205 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.43 % Allowed : 8.82 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1932 helix: 1.19 (0.24), residues: 453 sheet: 0.93 (0.21), residues: 561 loop : 0.90 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 473 HIS 0.005 0.001 HIS D 30 PHE 0.013 0.002 PHE C 111 TYR 0.018 0.002 TYR I 117 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00897 ( 3) link_NAG-ASN : angle 1.93458 ( 9) hydrogen bonds : bond 0.05506 ( 754) hydrogen bonds : angle 5.43848 ( 2079) SS BOND : bond 0.00239 ( 24) SS BOND : angle 1.36106 ( 48) covalent geometry : bond 0.00334 (15570) covalent geometry : angle 0.60690 (21084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8037 (tt0) cc_final: 0.7804 (tt0) REVERT: A 189 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.6620 (ttp-110) REVERT: A 193 GLU cc_start: 0.7545 (tt0) cc_final: 0.7256 (tt0) REVERT: A 462 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8247 (ttmm) REVERT: A 466 ASP cc_start: 0.8085 (m-30) cc_final: 0.7840 (m-30) REVERT: B 189 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6730 (ttp-110) REVERT: B 193 GLU cc_start: 0.7380 (tt0) cc_final: 0.7162 (tt0) REVERT: B 287 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7969 (ttt-90) REVERT: B 406 ASP cc_start: 0.8280 (p0) cc_final: 0.8056 (p0) REVERT: B 468 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 466 ASP cc_start: 0.8091 (m-30) cc_final: 0.7783 (m-30) outliers start: 41 outliers final: 14 residues processed: 333 average time/residue: 1.4603 time to fit residues: 529.8604 Evaluate side-chains 320 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 306 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 70 GLN B 447 ASN C 42 GLN C 67 GLN C 290 ASN C 304 GLN C 399 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111381 restraints weight = 20231.699| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.00 r_work: 0.3297 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15597 Z= 0.183 Angle : 0.602 9.415 21141 Z= 0.315 Chirality : 0.046 0.155 2460 Planarity : 0.004 0.036 2700 Dihedral : 4.787 23.478 2205 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.72 % Allowed : 10.72 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1932 helix: 1.52 (0.25), residues: 453 sheet: 0.80 (0.20), residues: 558 loop : 0.80 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 473 HIS 0.005 0.001 HIS D 30 PHE 0.016 0.002 PHE C 346 TYR 0.018 0.002 TYR I 117 ARG 0.010 0.000 ARG C 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 3) link_NAG-ASN : angle 1.87602 ( 9) hydrogen bonds : bond 0.05069 ( 754) hydrogen bonds : angle 5.11268 ( 2079) SS BOND : bond 0.00378 ( 24) SS BOND : angle 1.53720 ( 48) covalent geometry : bond 0.00446 (15570) covalent geometry : angle 0.59729 (21084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8035 (tt0) cc_final: 0.7747 (tt0) REVERT: A 175 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7218 (m) REVERT: A 189 ARG cc_start: 0.6998 (ttp-110) cc_final: 0.6646 (ttp-110) REVERT: A 193 GLU cc_start: 0.7478 (tt0) cc_final: 0.7185 (tt0) REVERT: G 117 TYR cc_start: 0.8813 (m-80) cc_final: 0.8485 (m-80) REVERT: B 24 LYS cc_start: 0.8443 (mtpm) cc_final: 0.8149 (mtpm) REVERT: B 136 GLU cc_start: 0.8145 (tt0) cc_final: 0.7926 (tt0) REVERT: B 189 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6810 (ttp-110) REVERT: B 193 GLU cc_start: 0.7375 (tt0) cc_final: 0.7164 (tt0) REVERT: B 255 ASP cc_start: 0.8092 (m-30) cc_final: 0.7870 (m-30) REVERT: B 287 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7962 (ttt-90) REVERT: B 473 TRP cc_start: 0.6960 (m-10) cc_final: 0.6696 (m-90) REVERT: C 466 ASP cc_start: 0.8118 (m-30) cc_final: 0.7780 (m-30) outliers start: 46 outliers final: 18 residues processed: 335 average time/residue: 1.4170 time to fit residues: 517.2282 Evaluate side-chains 328 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 309 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 96 optimal weight: 0.0770 chunk 184 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 447 ASN C 399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112141 restraints weight = 20216.576| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.01 r_work: 0.3305 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15597 Z= 0.142 Angle : 0.557 9.405 21141 Z= 0.290 Chirality : 0.044 0.139 2460 Planarity : 0.004 0.034 2700 Dihedral : 4.539 21.204 2205 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.66 % Allowed : 12.26 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 1932 helix: 1.74 (0.25), residues: 453 sheet: 0.70 (0.20), residues: 573 loop : 0.76 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 473 HIS 0.004 0.001 HIS D 30 PHE 0.014 0.002 PHE C 346 TYR 0.014 0.002 TYR B 294 ARG 0.006 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 3) link_NAG-ASN : angle 1.71407 ( 9) hydrogen bonds : bond 0.04340 ( 754) hydrogen bonds : angle 4.91118 ( 2079) SS BOND : bond 0.00351 ( 24) SS BOND : angle 1.27849 ( 48) covalent geometry : bond 0.00338 (15570) covalent geometry : angle 0.55312 (21084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7017 (ttp-110) cc_final: 0.6653 (ttp-110) REVERT: A 193 GLU cc_start: 0.7403 (tt0) cc_final: 0.7124 (tt0) REVERT: B 136 GLU cc_start: 0.8128 (tt0) cc_final: 0.7885 (tt0) REVERT: B 189 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6902 (ttp-110) REVERT: B 287 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7948 (ttt-90) REVERT: C 351 GLU cc_start: 0.8247 (mp0) cc_final: 0.7666 (mp0) REVERT: C 466 ASP cc_start: 0.8114 (m-30) cc_final: 0.7806 (m-30) outliers start: 45 outliers final: 20 residues processed: 331 average time/residue: 1.4536 time to fit residues: 523.6437 Evaluate side-chains 324 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 146 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 304 GLN B 447 ASN C 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112664 restraints weight = 20483.597| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.02 r_work: 0.3317 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15597 Z= 0.120 Angle : 0.541 8.688 21141 Z= 0.278 Chirality : 0.043 0.141 2460 Planarity : 0.003 0.033 2700 Dihedral : 4.341 21.198 2205 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.55 % Allowed : 13.44 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1932 helix: 1.80 (0.25), residues: 459 sheet: 0.71 (0.20), residues: 561 loop : 0.72 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 473 HIS 0.004 0.001 HIS B 206 PHE 0.013 0.001 PHE C 346 TYR 0.013 0.001 TYR A 294 ARG 0.005 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 3) link_NAG-ASN : angle 1.80942 ( 9) hydrogen bonds : bond 0.03935 ( 754) hydrogen bonds : angle 4.79999 ( 2079) SS BOND : bond 0.00180 ( 24) SS BOND : angle 1.13987 ( 48) covalent geometry : bond 0.00279 (15570) covalent geometry : angle 0.53751 (21084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 309 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6653 (ttp-110) REVERT: A 193 GLU cc_start: 0.7370 (tt0) cc_final: 0.7072 (tt0) REVERT: A 255 ASP cc_start: 0.7946 (m-30) cc_final: 0.7739 (m-30) REVERT: B 189 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6987 (ttp-110) REVERT: B 287 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7926 (ttt-90) REVERT: C 77 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8166 (mtm180) REVERT: C 351 GLU cc_start: 0.8268 (mp0) cc_final: 0.7714 (mp0) REVERT: C 466 ASP cc_start: 0.8125 (m-30) cc_final: 0.7746 (m-30) outliers start: 43 outliers final: 24 residues processed: 323 average time/residue: 1.4669 time to fit residues: 518.2060 Evaluate side-chains 327 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 139 optimal weight: 4.9990 chunk 42 optimal weight: 0.0040 chunk 145 optimal weight: 1.9990 chunk 128 optimal weight: 0.0000 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 418 ASN B 70 GLN B 290 ASN B 304 GLN B 447 ASN C 399 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113831 restraints weight = 20289.665| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.02 r_work: 0.3326 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15597 Z= 0.109 Angle : 0.537 10.181 21141 Z= 0.275 Chirality : 0.043 0.142 2460 Planarity : 0.003 0.038 2700 Dihedral : 4.188 20.725 2205 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.66 % Allowed : 13.91 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1932 helix: 1.96 (0.25), residues: 459 sheet: 0.74 (0.20), residues: 561 loop : 0.70 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS C 206 PHE 0.012 0.001 PHE C 346 TYR 0.012 0.001 TYR A 294 ARG 0.012 0.000 ARG C 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 3) link_NAG-ASN : angle 1.87984 ( 9) hydrogen bonds : bond 0.03670 ( 754) hydrogen bonds : angle 4.70778 ( 2079) SS BOND : bond 0.00192 ( 24) SS BOND : angle 1.04585 ( 48) covalent geometry : bond 0.00251 (15570) covalent geometry : angle 0.53417 (21084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7031 (ttp-110) cc_final: 0.6640 (ttp-110) REVERT: A 193 GLU cc_start: 0.7278 (tt0) cc_final: 0.7008 (tt0) REVERT: A 319 LYS cc_start: 0.8234 (mtmm) cc_final: 0.8010 (mtmm) REVERT: B 189 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.7021 (ttp-110) REVERT: B 287 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7906 (ttt-90) REVERT: C 77 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.8099 (mtm180) REVERT: C 351 GLU cc_start: 0.8264 (mp0) cc_final: 0.7726 (mp0) REVERT: C 468 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 473 TRP cc_start: 0.6843 (m-10) cc_final: 0.6545 (m-90) outliers start: 45 outliers final: 27 residues processed: 332 average time/residue: 1.3607 time to fit residues: 493.5729 Evaluate side-chains 328 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 146 optimal weight: 0.0570 chunk 27 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 290 ASN B 304 GLN B 447 ASN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.114136 restraints weight = 20549.193| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.02 r_work: 0.3333 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15597 Z= 0.102 Angle : 0.538 12.323 21141 Z= 0.272 Chirality : 0.043 0.167 2460 Planarity : 0.003 0.031 2700 Dihedral : 4.084 20.164 2205 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.61 % Allowed : 14.62 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 1932 helix: 2.10 (0.25), residues: 459 sheet: 0.80 (0.20), residues: 561 loop : 0.70 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS B 206 PHE 0.012 0.001 PHE C 346 TYR 0.012 0.001 TYR A 294 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 3) link_NAG-ASN : angle 2.20031 ( 9) hydrogen bonds : bond 0.03438 ( 754) hydrogen bonds : angle 4.64866 ( 2079) SS BOND : bond 0.00217 ( 24) SS BOND : angle 0.95797 ( 48) covalent geometry : bond 0.00233 (15570) covalent geometry : angle 0.53439 (21084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7052 (ttp-110) cc_final: 0.6645 (ttp-110) REVERT: A 193 GLU cc_start: 0.7290 (tt0) cc_final: 0.7038 (tt0) REVERT: B 287 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.7882 (ttt-90) REVERT: C 351 GLU cc_start: 0.8281 (mp0) cc_final: 0.7707 (mp0) REVERT: C 466 ASP cc_start: 0.8149 (m-30) cc_final: 0.7725 (m-30) REVERT: C 468 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 473 TRP cc_start: 0.6854 (m-10) cc_final: 0.6574 (m-90) outliers start: 44 outliers final: 31 residues processed: 330 average time/residue: 1.4435 time to fit residues: 520.8426 Evaluate side-chains 337 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 185 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 418 ASN B 70 GLN B 290 ASN B 447 ASN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111996 restraints weight = 20300.344| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.01 r_work: 0.3309 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15597 Z= 0.175 Angle : 0.587 12.460 21141 Z= 0.296 Chirality : 0.045 0.248 2460 Planarity : 0.004 0.033 2700 Dihedral : 4.216 18.546 2205 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.66 % Allowed : 14.86 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 1932 helix: 2.07 (0.25), residues: 459 sheet: 0.79 (0.20), residues: 558 loop : 0.60 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 118 HIS 0.003 0.001 HIS D 30 PHE 0.015 0.002 PHE C 346 TYR 0.015 0.002 TYR B 294 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 3) link_NAG-ASN : angle 2.76753 ( 9) hydrogen bonds : bond 0.03972 ( 754) hydrogen bonds : angle 4.71952 ( 2079) SS BOND : bond 0.00239 ( 24) SS BOND : angle 1.23568 ( 48) covalent geometry : bond 0.00432 (15570) covalent geometry : angle 0.58227 (21084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6642 (ttp-110) REVERT: A 193 GLU cc_start: 0.7312 (tt0) cc_final: 0.7051 (tt0) REVERT: B 287 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7941 (ttt-90) REVERT: C 351 GLU cc_start: 0.8281 (mp0) cc_final: 0.7684 (mp0) REVERT: C 466 ASP cc_start: 0.8176 (m-30) cc_final: 0.7710 (m-30) REVERT: C 473 TRP cc_start: 0.6883 (m-10) cc_final: 0.6614 (m-90) outliers start: 45 outliers final: 29 residues processed: 319 average time/residue: 1.4022 time to fit residues: 486.9248 Evaluate side-chains 329 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 155 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112718 restraints weight = 20380.220| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.02 r_work: 0.3316 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15597 Z= 0.138 Angle : 0.576 13.001 21141 Z= 0.289 Chirality : 0.044 0.300 2460 Planarity : 0.003 0.033 2700 Dihedral : 4.205 17.948 2205 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1932 helix: 2.08 (0.25), residues: 459 sheet: 0.79 (0.20), residues: 558 loop : 0.59 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 118 HIS 0.003 0.001 HIS C 206 PHE 0.014 0.001 PHE C 346 TYR 0.014 0.002 TYR A 294 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 3) link_NAG-ASN : angle 2.98991 ( 9) hydrogen bonds : bond 0.03759 ( 754) hydrogen bonds : angle 4.70991 ( 2079) SS BOND : bond 0.00213 ( 24) SS BOND : angle 1.10279 ( 48) covalent geometry : bond 0.00337 (15570) covalent geometry : angle 0.57083 (21084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.6641 (ttp-110) REVERT: A 193 GLU cc_start: 0.7283 (tt0) cc_final: 0.7024 (tt0) REVERT: A 435 LEU cc_start: 0.8220 (tp) cc_final: 0.7909 (tp) REVERT: B 287 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7888 (ttt-90) REVERT: C 351 GLU cc_start: 0.8298 (mp0) cc_final: 0.7716 (mp0) REVERT: C 466 ASP cc_start: 0.8178 (m-30) cc_final: 0.7717 (m-30) REVERT: C 468 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7370 (mm-30) REVERT: C 473 TRP cc_start: 0.6806 (m-10) cc_final: 0.6566 (m-90) outliers start: 37 outliers final: 30 residues processed: 318 average time/residue: 1.5477 time to fit residues: 537.6177 Evaluate side-chains 333 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 155 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113535 restraints weight = 20442.531| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.04 r_work: 0.3323 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15597 Z= 0.123 Angle : 0.573 13.884 21141 Z= 0.286 Chirality : 0.044 0.382 2460 Planarity : 0.003 0.032 2700 Dihedral : 4.193 19.112 2205 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.89 % Allowed : 15.75 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1932 helix: 1.99 (0.24), residues: 477 sheet: 0.82 (0.21), residues: 540 loop : 0.63 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 118 HIS 0.004 0.001 HIS C 206 PHE 0.013 0.001 PHE C 346 TYR 0.012 0.001 TYR A 294 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 3) link_NAG-ASN : angle 3.53215 ( 9) hydrogen bonds : bond 0.03617 ( 754) hydrogen bonds : angle 4.67569 ( 2079) SS BOND : bond 0.00194 ( 24) SS BOND : angle 1.00708 ( 48) covalent geometry : bond 0.00295 (15570) covalent geometry : angle 0.56667 (21084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 303 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7006 (ttp-110) cc_final: 0.6609 (ttp-110) REVERT: A 193 GLU cc_start: 0.7300 (tt0) cc_final: 0.7050 (tt0) REVERT: A 351 GLU cc_start: 0.8325 (mp0) cc_final: 0.7976 (mp0) REVERT: A 435 LEU cc_start: 0.8215 (tp) cc_final: 0.7901 (tp) REVERT: B 287 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7926 (ttt-90) REVERT: C 351 GLU cc_start: 0.8300 (mp0) cc_final: 0.7724 (mp0) REVERT: C 466 ASP cc_start: 0.8179 (m-30) cc_final: 0.7706 (m-30) REVERT: C 468 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 473 TRP cc_start: 0.6796 (m-10) cc_final: 0.6587 (m-90) outliers start: 32 outliers final: 27 residues processed: 314 average time/residue: 1.5198 time to fit residues: 516.9728 Evaluate side-chains 322 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 295 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 119 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 79 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 155 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN C 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112763 restraints weight = 20256.691| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.03 r_work: 0.3320 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15597 Z= 0.144 Angle : 0.598 13.969 21141 Z= 0.294 Chirality : 0.045 0.565 2460 Planarity : 0.004 0.033 2700 Dihedral : 4.197 19.145 2205 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.89 % Allowed : 16.28 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1932 helix: 2.01 (0.24), residues: 477 sheet: 0.85 (0.21), residues: 537 loop : 0.60 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 118 HIS 0.003 0.001 HIS D 30 PHE 0.014 0.001 PHE C 346 TYR 0.014 0.002 TYR A 294 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 3) link_NAG-ASN : angle 6.38294 ( 9) hydrogen bonds : bond 0.03743 ( 754) hydrogen bonds : angle 4.67208 ( 2079) SS BOND : bond 0.00223 ( 24) SS BOND : angle 1.05114 ( 48) covalent geometry : bond 0.00352 (15570) covalent geometry : angle 0.58162 (21084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14449.81 seconds wall clock time: 248 minutes 16.10 seconds (14896.10 seconds total)