Starting phenix.real_space_refine on Thu Sep 18 17:59:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v5k_42983/09_2025/8v5k_42983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v5k_42983/09_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_42983/09_2025/8v5k_42983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v5k_42983/09_2025/8v5k_42983.map" model { file = "/net/cci-nas-00/data/ceres_data/8v5k_42983/09_2025/8v5k_42983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v5k_42983/09_2025/8v5k_42983.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.18, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 492.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.50 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: 2.52 Time building geometry restraints manager: 1.31 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.059 0.002 ARG B 281 TYR 0.044 0.004 TYR I 117 PHE 0.027 0.003 PHE C 111 TRP 0.024 0.003 TRP C 473 HIS 0.008 0.002 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00685 (15570) covalent geometry : angle 0.75159 (21084) SS BOND : bond 0.00375 ( 24) SS BOND : angle 0.89682 ( 48) hydrogen bonds : bond 0.21618 ( 754) hydrogen bonds : angle 7.77288 ( 2079) link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 1.77805 ( 9) *********************** 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 : 0.433 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: 0.6677 time to fit residues: 270.4485 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 : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.137881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111507 restraints weight = 20253.324| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.00 r_work: 0.3307 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15597 Z= 0.161 Angle : 0.618 10.316 21141 Z= 0.330 Chirality : 0.046 0.193 2460 Planarity : 0.004 0.035 2700 Dihedral : 5.160 32.007 2205 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.55 % Allowed : 8.82 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 1932 helix: 1.18 (0.24), residues: 453 sheet: 0.92 (0.21), residues: 561 loop : 0.88 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 306 TYR 0.020 0.002 TYR I 117 PHE 0.014 0.002 PHE C 111 TRP 0.023 0.002 TRP C 473 HIS 0.005 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00369 (15570) covalent geometry : angle 0.61389 (21084) SS BOND : bond 0.00375 ( 24) SS BOND : angle 1.35125 ( 48) hydrogen bonds : bond 0.05403 ( 754) hydrogen bonds : angle 5.40245 ( 2079) link_NAG-ASN : bond 0.00974 ( 3) link_NAG-ASN : angle 1.89688 ( 9) *********************** 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 364 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6938 (ttp-110) cc_final: 0.6646 (ttp-110) REVERT: A 193 GLU cc_start: 0.7545 (tt0) cc_final: 0.7255 (tt0) REVERT: A 462 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8258 (ttmm) REVERT: A 466 ASP cc_start: 0.8103 (m-30) cc_final: 0.7864 (m-30) REVERT: B 189 ARG cc_start: 0.7103 (ttp-110) cc_final: 0.6782 (ttp-110) REVERT: B 193 GLU cc_start: 0.7361 (tt0) cc_final: 0.7137 (tt0) REVERT: B 287 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7913 (ttt-90) REVERT: B 406 ASP cc_start: 0.8281 (p0) cc_final: 0.8055 (p0) REVERT: B 468 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 466 ASP cc_start: 0.8100 (m-30) cc_final: 0.7798 (m-30) outliers start: 43 outliers final: 13 residues processed: 335 average time/residue: 0.6623 time to fit residues: 240.6023 Evaluate side-chains 325 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 312 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 chunk 69 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 42 GLN B 70 GLN B 447 ASN C 290 ASN C 304 GLN C 399 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112611 restraints weight = 20424.108| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.01 r_work: 0.3310 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1740 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= 0.141 Angle : 0.572 8.416 21141 Z= 0.300 Chirality : 0.045 0.142 2460 Planarity : 0.004 0.033 2700 Dihedral : 4.672 22.504 2205 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.61 % Allowed : 11.07 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.19), residues: 1932 helix: 1.59 (0.25), residues: 453 sheet: 0.83 (0.20), residues: 561 loop : 0.87 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 189 TYR 0.014 0.002 TYR C 71 PHE 0.014 0.002 PHE C 346 TRP 0.015 0.001 TRP C 473 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00333 (15570) covalent geometry : angle 0.56826 (21084) SS BOND : bond 0.00298 ( 24) SS BOND : angle 1.24582 ( 48) hydrogen bonds : bond 0.04694 ( 754) hydrogen bonds : angle 5.04037 ( 2079) link_NAG-ASN : bond 0.00960 ( 3) link_NAG-ASN : angle 1.80535 ( 9) *********************** 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 354 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7233 (m) REVERT: A 189 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6629 (ttp-110) REVERT: A 193 GLU cc_start: 0.7447 (tt0) cc_final: 0.7149 (tt0) REVERT: B 136 GLU cc_start: 0.8125 (tt0) cc_final: 0.7909 (tt0) REVERT: B 189 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6817 (ttp-110) REVERT: B 193 GLU cc_start: 0.7346 (tt0) cc_final: 0.7132 (tt0) REVERT: B 287 ARG cc_start: 0.8176 (ttt-90) cc_final: 0.7924 (ttt-90) REVERT: B 462 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8174 (ttmm) REVERT: B 473 TRP cc_start: 0.6972 (m-10) cc_final: 0.6711 (m-90) REVERT: C 466 ASP cc_start: 0.8096 (m-30) cc_final: 0.7763 (m-30) outliers start: 44 outliers final: 15 residues processed: 330 average time/residue: 0.6404 time to fit residues: 228.7057 Evaluate side-chains 316 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL 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 58 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 234 LEU 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 261 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain E residue 39 MET 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 68 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 42 GLN B 70 GLN B 447 ASN C 42 GLN C 290 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 = 0.3796 r_free = 0.3796 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111631 restraints weight = 20248.790| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.00 r_work: 0.3303 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15597 Z= 0.161 Angle : 0.568 9.399 21141 Z= 0.295 Chirality : 0.044 0.141 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.517 21.060 2205 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.66 % Allowed : 12.43 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 1932 helix: 1.77 (0.25), residues: 453 sheet: 0.71 (0.20), residues: 573 loop : 0.76 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 306 TYR 0.015 0.002 TYR B 294 PHE 0.016 0.002 PHE C 346 TRP 0.012 0.001 TRP B 473 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00389 (15570) covalent geometry : angle 0.56400 (21084) SS BOND : bond 0.00244 ( 24) SS BOND : angle 1.31728 ( 48) hydrogen bonds : bond 0.04397 ( 754) hydrogen bonds : angle 4.89871 ( 2079) link_NAG-ASN : bond 0.00684 ( 3) link_NAG-ASN : angle 1.76790 ( 9) *********************** 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 358 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6647 (ttp-110) REVERT: A 193 GLU cc_start: 0.7387 (tt0) cc_final: 0.7110 (tt0) REVERT: D 85 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7839 (mtm) REVERT: B 136 GLU cc_start: 0.8136 (tt0) cc_final: 0.7901 (tt0) REVERT: B 189 ARG cc_start: 0.7224 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: B 287 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7928 (ttt-90) REVERT: C 351 GLU cc_start: 0.8248 (mp0) cc_final: 0.7667 (mp0) outliers start: 45 outliers final: 19 residues processed: 333 average time/residue: 0.6043 time to fit residues: 218.4806 Evaluate side-chains 323 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain D residue 85 MET 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 G residue 116 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 347 VAL 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 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 68 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 42 GLN C 290 ASN C 399 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111491 restraints weight = 20373.456| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.01 r_work: 0.3293 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15597 Z= 0.191 Angle : 0.589 10.035 21141 Z= 0.302 Chirality : 0.045 0.180 2460 Planarity : 0.004 0.036 2700 Dihedral : 4.510 20.630 2205 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.84 % Allowed : 13.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 1932 helix: 1.78 (0.24), residues: 453 sheet: 0.65 (0.20), residues: 573 loop : 0.67 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 306 TYR 0.016 0.002 TYR A 294 PHE 0.017 0.002 PHE C 346 TRP 0.008 0.001 TRP C 473 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00470 (15570) covalent geometry : angle 0.58456 (21084) SS BOND : bond 0.00261 ( 24) SS BOND : angle 1.34705 ( 48) hydrogen bonds : bond 0.04475 ( 754) hydrogen bonds : angle 4.90214 ( 2079) link_NAG-ASN : bond 0.00717 ( 3) link_NAG-ASN : angle 1.95482 ( 9) *********************** 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 351 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7040 (ttp-110) cc_final: 0.6658 (ttp-110) REVERT: A 193 GLU cc_start: 0.7421 (tt0) cc_final: 0.7137 (tt0) REVERT: A 466 ASP cc_start: 0.8102 (m-30) cc_final: 0.7771 (m-30) REVERT: B 189 ARG cc_start: 0.7245 (ttp-110) cc_final: 0.6973 (ttp-110) REVERT: B 287 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7979 (ttt-90) REVERT: C 189 ARG cc_start: 0.7031 (ttp-110) cc_final: 0.6830 (ttp-110) REVERT: C 351 GLU cc_start: 0.8255 (mp0) cc_final: 0.7655 (mp0) REVERT: C 466 ASP cc_start: 0.8074 (m-30) cc_final: 0.7689 (m-30) outliers start: 48 outliers final: 25 residues processed: 321 average time/residue: 0.6369 time to fit residues: 221.5699 Evaluate side-chains 331 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 ASN 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 36 ILE Chi-restraints excluded: chain G residue 58 SER 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 314 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 234 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 113 THR 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 180 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 290 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 = 0.3794 r_free = 0.3794 target = 0.138089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111580 restraints weight = 20337.009| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.02 r_work: 0.3293 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15597 Z= 0.174 Angle : 0.578 9.977 21141 Z= 0.295 Chirality : 0.045 0.154 2460 Planarity : 0.004 0.036 2700 Dihedral : 4.442 19.837 2205 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.20 % Allowed : 13.50 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 1932 helix: 1.83 (0.24), residues: 453 sheet: 0.66 (0.20), residues: 561 loop : 0.64 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.016 0.002 TYR A 294 PHE 0.015 0.002 PHE C 346 TRP 0.008 0.001 TRP G 118 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00429 (15570) covalent geometry : angle 0.57399 (21084) SS BOND : bond 0.00239 ( 24) SS BOND : angle 1.22392 ( 48) hydrogen bonds : bond 0.04298 ( 754) hydrogen bonds : angle 4.85634 ( 2079) link_NAG-ASN : bond 0.00671 ( 3) link_NAG-ASN : angle 2.13563 ( 9) *********************** 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 369 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6657 (ttp-110) REVERT: A 193 GLU cc_start: 0.7340 (tt0) cc_final: 0.7061 (tt0) REVERT: B 21 ASP cc_start: 0.7756 (t0) cc_final: 0.7502 (t0) REVERT: B 136 GLU cc_start: 0.8115 (tt0) cc_final: 0.7876 (tt0) REVERT: B 139 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7643 (tp40) REVERT: B 189 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6987 (ttp-110) REVERT: B 287 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7963 (ttt-90) REVERT: C 189 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6823 (ttp-110) REVERT: C 351 GLU cc_start: 0.8279 (mp0) cc_final: 0.7666 (mp0) REVERT: C 466 ASP cc_start: 0.8095 (m-30) cc_final: 0.7615 (m-30) REVERT: C 473 TRP cc_start: 0.6849 (m-10) cc_final: 0.6502 (m-90) outliers start: 54 outliers final: 32 residues processed: 335 average time/residue: 0.6220 time to fit residues: 226.6129 Evaluate side-chains 335 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 302 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 402 ASN 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 36 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain B residue 139 GLN 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 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 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 296 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 113 THR 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 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN A 418 ASN B 70 GLN B 290 ASN B 447 ASN C 290 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 = 0.3796 r_free = 0.3796 target = 0.138211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111788 restraints weight = 20135.295| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.00 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2207 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= 0.165 Angle : 0.582 11.389 21141 Z= 0.295 Chirality : 0.044 0.171 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.392 20.035 2205 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.08 % Allowed : 14.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.19), residues: 1932 helix: 1.94 (0.24), residues: 453 sheet: 0.54 (0.20), residues: 570 loop : 0.66 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.016 0.002 TYR A 294 PHE 0.015 0.002 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00404 (15570) covalent geometry : angle 0.57785 (21084) SS BOND : bond 0.00234 ( 24) SS BOND : angle 1.20036 ( 48) hydrogen bonds : bond 0.04162 ( 754) hydrogen bonds : angle 4.82827 ( 2079) link_NAG-ASN : bond 0.00619 ( 3) link_NAG-ASN : angle 2.25293 ( 9) *********************** 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 361 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7023 (ttp-110) cc_final: 0.6638 (ttp-110) REVERT: A 193 GLU cc_start: 0.7330 (tt0) cc_final: 0.7037 (tt0) REVERT: D 85 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7660 (mtm) REVERT: B 136 GLU cc_start: 0.8116 (tt0) cc_final: 0.7891 (tt0) REVERT: B 189 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.7042 (ttp-110) REVERT: B 287 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7958 (ttt-90) REVERT: C 189 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6743 (ttp-110) REVERT: C 351 GLU cc_start: 0.8280 (mp0) cc_final: 0.7692 (mp0) REVERT: C 466 ASP cc_start: 0.8128 (m-30) cc_final: 0.7677 (m-30) REVERT: C 473 TRP cc_start: 0.6860 (m-10) cc_final: 0.6532 (m-90) outliers start: 52 outliers final: 31 residues processed: 327 average time/residue: 0.6216 time to fit residues: 220.7226 Evaluate side-chains 332 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 85 MET 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 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 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 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 113 THR 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 139 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 399 ASN A 418 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN C 290 ASN C 399 ASN C 447 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111803 restraints weight = 20470.694| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.03 r_work: 0.3303 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15597 Z= 0.156 Angle : 0.582 12.520 21141 Z= 0.295 Chirality : 0.044 0.197 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.346 19.005 2205 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.49 % Allowed : 15.28 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 1932 helix: 2.02 (0.25), residues: 453 sheet: 0.66 (0.20), residues: 561 loop : 0.60 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.016 0.002 TYR A 294 PHE 0.014 0.002 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.007 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00381 (15570) covalent geometry : angle 0.57783 (21084) SS BOND : bond 0.00213 ( 24) SS BOND : angle 1.09236 ( 48) hydrogen bonds : bond 0.04028 ( 754) hydrogen bonds : angle 4.79599 ( 2079) link_NAG-ASN : bond 0.00581 ( 3) link_NAG-ASN : angle 2.47803 ( 9) *********************** 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 343 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7001 (ttp-110) cc_final: 0.6629 (ttp-110) REVERT: A 193 GLU cc_start: 0.7377 (tt0) cc_final: 0.7091 (tt0) REVERT: A 435 LEU cc_start: 0.8219 (tp) cc_final: 0.7898 (tp) REVERT: D 85 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7734 (mtm) REVERT: B 136 GLU cc_start: 0.8111 (tt0) cc_final: 0.7896 (tt0) REVERT: B 189 ARG cc_start: 0.7283 (ttp-110) cc_final: 0.7022 (ttp-110) REVERT: B 287 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7985 (ttt-90) REVERT: C 189 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6714 (ttp-110) REVERT: C 351 GLU cc_start: 0.8273 (mp0) cc_final: 0.7681 (mp0) REVERT: C 466 ASP cc_start: 0.8121 (m-30) cc_final: 0.7676 (m-30) REVERT: C 468 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7361 (mm-30) REVERT: C 473 TRP cc_start: 0.6881 (m-10) cc_final: 0.6623 (m-90) outliers start: 42 outliers final: 33 residues processed: 316 average time/residue: 0.6292 time to fit residues: 215.8811 Evaluate side-chains 331 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 85 MET 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 36 ILE 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 407 GLN 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 253 ILE 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 113 THR 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 69 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 ASN B 70 GLN B 290 ASN B 418 ASN B 447 ASN C 290 ASN C 399 ASN C 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111789 restraints weight = 20243.170| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.02 r_work: 0.3306 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15597 Z= 0.163 Angle : 0.593 13.373 21141 Z= 0.298 Chirality : 0.045 0.236 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.344 19.379 2205 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.49 % Allowed : 15.75 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 1932 helix: 2.10 (0.25), residues: 453 sheet: 0.58 (0.21), residues: 549 loop : 0.57 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.015 0.002 TYR A 294 PHE 0.015 0.002 PHE C 346 TRP 0.008 0.001 TRP B 473 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00401 (15570) covalent geometry : angle 0.58878 (21084) SS BOND : bond 0.00224 ( 24) SS BOND : angle 1.16632 ( 48) hydrogen bonds : bond 0.04032 ( 754) hydrogen bonds : angle 4.78054 ( 2079) link_NAG-ASN : bond 0.00604 ( 3) link_NAG-ASN : angle 2.71116 ( 9) *********************** 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 343 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6963 (ttp-110) cc_final: 0.6577 (ttp-110) REVERT: A 193 GLU cc_start: 0.7435 (tt0) cc_final: 0.7150 (tt0) REVERT: D 85 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7705 (mtm) REVERT: B 189 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.7048 (ttp-110) REVERT: B 287 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7987 (ttt-90) REVERT: C 189 ARG cc_start: 0.7047 (ttp-110) cc_final: 0.6775 (ttp-110) REVERT: C 351 GLU cc_start: 0.8276 (mp0) cc_final: 0.7711 (mp0) REVERT: C 466 ASP cc_start: 0.8130 (m-30) cc_final: 0.7678 (m-30) REVERT: C 468 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7369 (mm-30) REVERT: C 473 TRP cc_start: 0.6867 (m-10) cc_final: 0.6619 (m-90) outliers start: 42 outliers final: 35 residues processed: 315 average time/residue: 0.6633 time to fit residues: 226.3242 Evaluate side-chains 333 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 85 MET 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 36 ILE 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 407 GLN 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 253 ILE 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 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 113 THR 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 113 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 290 ASN B 418 ASN B 447 ASN C 399 ASN C 447 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112102 restraints weight = 20429.591| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.03 r_work: 0.3304 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15597 Z= 0.163 Angle : 0.599 13.841 21141 Z= 0.300 Chirality : 0.045 0.285 2460 Planarity : 0.004 0.035 2700 Dihedral : 4.352 18.985 2205 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.43 % Allowed : 15.81 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 1932 helix: 2.13 (0.25), residues: 453 sheet: 0.60 (0.21), residues: 546 loop : 0.54 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.015 0.002 TYR A 294 PHE 0.015 0.002 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00403 (15570) covalent geometry : angle 0.59368 (21084) SS BOND : bond 0.00223 ( 24) SS BOND : angle 1.14005 ( 48) hydrogen bonds : bond 0.04013 ( 754) hydrogen bonds : angle 4.77690 ( 2079) link_NAG-ASN : bond 0.00568 ( 3) link_NAG-ASN : angle 3.01592 ( 9) ********************** 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 338 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.6938 (ttp-110) cc_final: 0.6546 (ttp-110) REVERT: A 193 GLU cc_start: 0.7457 (tt0) cc_final: 0.7159 (tt0) REVERT: D 85 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7685 (mtm) REVERT: B 189 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: B 287 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7996 (ttt-90) REVERT: B 415 LYS cc_start: 0.8454 (mttt) cc_final: 0.8251 (mttt) REVERT: C 189 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6780 (ttp-110) REVERT: C 351 GLU cc_start: 0.8283 (mp0) cc_final: 0.7711 (mp0) REVERT: C 466 ASP cc_start: 0.8149 (m-30) cc_final: 0.7685 (m-30) REVERT: C 468 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7369 (mm-30) REVERT: C 473 TRP cc_start: 0.6793 (m-10) cc_final: 0.6578 (m-90) outliers start: 41 outliers final: 36 residues processed: 310 average time/residue: 0.6950 time to fit residues: 233.0430 Evaluate side-chains 331 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 85 MET 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 36 ILE 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 317 MET 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 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 347 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain E residue 113 THR 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 82 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 159 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113131 restraints weight = 20111.825| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.01 r_work: 0.3319 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15597 Z= 0.131 Angle : 0.584 13.263 21141 Z= 0.291 Chirality : 0.044 0.397 2460 Planarity : 0.003 0.035 2700 Dihedral : 4.295 18.515 2205 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.07 % Allowed : 16.52 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 1932 helix: 1.96 (0.24), residues: 483 sheet: 0.59 (0.21), residues: 549 loop : 0.67 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 306 TYR 0.013 0.001 TYR B 274 PHE 0.013 0.001 PHE C 346 TRP 0.008 0.001 TRP H 118 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00317 (15570) covalent geometry : angle 0.57794 (21084) SS BOND : bond 0.00193 ( 24) SS BOND : angle 1.02905 ( 48) hydrogen bonds : bond 0.03750 ( 754) hydrogen bonds : angle 4.72970 ( 2079) link_NAG-ASN : bond 0.00556 ( 3) link_NAG-ASN : angle 3.49004 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6656.23 seconds wall clock time: 113 minutes 39.18 seconds (6819.18 seconds total)