Starting phenix.real_space_refine on Thu Sep 18 03:06:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9e_44380/09_2025/9b9e_44380.cif" } resolution = 3.66 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= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8538 2.51 5 N 2250 2.21 5 O 2682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 13542 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "B" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "C" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3512 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.26, per 1000 atoms: 0.24 Number of scatterers: 13542 At special positions: 0 Unit cell: (114.4, 119.2, 120.8, 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 72 16.00 O 2682 8.00 N 2250 7.00 C 8538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 95 " 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 501 " - " ASN A 464 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 67 " " NAG B 501 " - " ASN B 414 " " NAG B 502 " - " ASN B 99 " " NAG B 503 " - " ASN B 464 " " NAG B 504 " - " ASN B 67 " " NAG C 501 " - " ASN C 414 " " NAG C 502 " - " ASN C 99 " " NAG C 503 " - " ASN C 464 " " NAG C 504 " - " ASN C 67 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 648.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 24 sheets defined 35.5% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.870A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.760A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.316A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.791A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.530A pdb=" N THR A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.956A pdb=" N ALA A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.685A pdb=" N GLY A 236 " --> pdb=" O GLN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.507A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.900A pdb=" N CYS A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.744A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 removed outlier: 4.399A pdb=" N SER A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.912A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.814A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 removed outlier: 3.757A pdb=" N GLY B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 4.185A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.733A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.819A pdb=" N THR B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.883A pdb=" N ALA B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 removed outlier: 3.701A pdb=" N GLY B 236 " --> pdb=" O GLN B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.543A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 removed outlier: 4.003A pdb=" N CYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.709A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 removed outlier: 4.070A pdb=" N SER B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 473 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.828A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 removed outlier: 3.811A pdb=" N SER C 69 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 100 removed outlier: 3.791A pdb=" N GLY C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 4.175A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.684A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.583A pdb=" N SER C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.679A pdb=" N THR C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.896A pdb=" N ALA C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 236 removed outlier: 3.716A pdb=" N GLY C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.551A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.988A pdb=" N CYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.749A pdb=" N GLY C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 481 removed outlier: 4.059A pdb=" N SER C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.909A pdb=" N PHE D 28 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER D 29 " --> pdb=" O ARG D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 29' Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.599A pdb=" N THR D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.811A pdb=" N PHE E 28 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 29 " --> pdb=" O ARG E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.524A pdb=" N THR E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.813A pdb=" N PHE F 28 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER F 29 " --> pdb=" O ARG F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.541A pdb=" N THR F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 7.905A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 162 removed outlier: 11.530A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.637A pdb=" N VAL A 113 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER C 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET A 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 249 removed outlier: 7.220A pdb=" N VAL D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET D 33 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY D 9 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N SER D 123 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 11 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 249 removed outlier: 7.220A pdb=" N VAL D 47 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET D 33 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'A' and resid 419 through 422 removed outlier: 4.594A pdb=" N ILE A 426 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 332 through 333 removed outlier: 7.868A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS B 45 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ALA B 291 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N LYS B 47 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N GLN B 289 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 162 removed outlier: 11.569A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 248 through 249 removed outlier: 7.301A pdb=" N VAL E 47 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 33 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY E 9 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER E 123 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL E 11 " --> pdb=" O SER E 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 248 through 249 removed outlier: 7.301A pdb=" N VAL E 47 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET E 33 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB7, first strand: chain 'B' and resid 419 through 422 removed outlier: 4.491A pdb=" N ILE B 426 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 332 through 333 removed outlier: 7.917A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LYS C 47 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLN C 289 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 162 removed outlier: 11.570A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 248 through 249 removed outlier: 7.347A pdb=" N VAL F 47 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET F 33 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY F 9 " --> pdb=" O THR F 121 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N SER F 123 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL F 11 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 248 through 249 removed outlier: 7.347A pdb=" N VAL F 47 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET F 33 " --> pdb=" O ARG F 49 " (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 'D' and resid 4 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 6 639 hydrogen bonds defined for protein. 1698 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: 2.55 Time building geometry restraints manager: 1.40 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: 4381 1.34 - 1.46: 2570 1.46 - 1.58: 6699 1.58 - 1.70: 0 1.70 - 1.81: 108 Bond restraints: 13758 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CB CYS C 355 " pdb=" SG CYS C 355 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.79e+00 ... (remaining 13753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 17408 1.72 - 3.43: 1105 3.43 - 5.15: 124 5.15 - 6.87: 32 6.87 - 8.58: 15 Bond angle restraints: 18684 Sorted by residual: angle pdb=" N ASN B 51 " pdb=" CA ASN B 51 " pdb=" C ASN B 51 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" N ASN C 51 " pdb=" CA ASN C 51 " pdb=" C ASN C 51 " ideal model delta sigma weight residual 109.81 118.15 -8.34 2.21e+00 2.05e-01 1.42e+01 angle pdb=" C ILE C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta sigma weight residual 120.82 126.36 -5.54 1.47e+00 4.63e-01 1.42e+01 angle pdb=" C ILE B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta sigma weight residual 120.82 126.25 -5.43 1.47e+00 4.63e-01 1.36e+01 angle pdb=" N GLY C 358 " pdb=" CA GLY C 358 " pdb=" C GLY C 358 " ideal model delta sigma weight residual 115.27 120.21 -4.94 1.41e+00 5.03e-01 1.23e+01 ... (remaining 18679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7947 17.94 - 35.88: 442 35.88 - 53.83: 96 53.83 - 71.77: 18 71.77 - 89.71: 17 Dihedral angle restraints: 8520 sinusoidal: 3471 harmonic: 5049 Sorted by residual: dihedral pdb=" CB CYS C 355 " pdb=" SG CYS C 355 " pdb=" SG CYS C 363 " pdb=" CB CYS C 363 " ideal model delta sinusoidal sigma weight residual -86.00 -135.01 49.01 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -134.77 48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 363 " pdb=" CB CYS A 363 " ideal model delta sinusoidal sigma weight residual -86.00 -133.78 47.78 1 1.00e+01 1.00e-02 3.15e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1626 0.063 - 0.125: 558 0.125 - 0.188: 56 0.188 - 0.251: 12 0.251 - 0.313: 4 Chirality restraints: 2256 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 99 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ASN A 99 " pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CB ASN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASN B 99 " pdb=" N ASN B 99 " pdb=" C ASN B 99 " pdb=" CB ASN B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2253 not shown) Planarity restraints: 2373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 99 " -0.030 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN A 99 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 99 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 99 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.012 2.00e-02 2.50e+03 2.13e-02 9.04e+00 pdb=" CG TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 49 " 0.223 9.50e-02 1.11e+02 1.00e-01 7.27e+00 pdb=" NE ARG F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG F 49 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG F 49 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 49 " 0.002 2.00e-02 2.50e+03 ... (remaining 2370 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4316 2.84 - 3.36: 13195 3.36 - 3.87: 20996 3.87 - 4.39: 23697 4.39 - 4.90: 41395 Nonbonded interactions: 103599 Sorted by model distance: nonbonded pdb=" OG1 THR B 334 " pdb=" O SER B 337 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR C 334 " pdb=" O SER C 337 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.367 3.040 nonbonded pdb=" OD1 ASP B 413 " pdb=" OG1 THR B 415 " model vdw 2.420 3.040 nonbonded pdb=" O ASN A 320 " pdb=" OG1 THR A 321 " model vdw 2.421 3.040 ... (remaining 103594 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: 0.01 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.008 0.056 13788 Z= 0.329 Angle : 0.977 13.358 18756 Z= 0.539 Chirality : 0.060 0.313 2256 Planarity : 0.007 0.100 2361 Dihedral : 12.544 89.710 5226 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.18), residues: 1728 helix: -1.47 (0.21), residues: 480 sheet: -0.14 (0.24), residues: 411 loop : -0.74 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG F 49 TYR 0.032 0.005 TYR A 206 PHE 0.016 0.002 PHE B 376 TRP 0.028 0.005 TRP F 114 HIS 0.005 0.002 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00792 (13758) covalent geometry : angle 0.94181 (18684) SS BOND : bond 0.00485 ( 18) SS BOND : angle 2.10137 ( 36) hydrogen bonds : bond 0.19958 ( 591) hydrogen bonds : angle 8.88990 ( 1698) link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 5.66119 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7967 (tp30) cc_final: 0.6724 (tt0) REVERT: A 139 LYS cc_start: 0.8061 (tptt) cc_final: 0.7318 (mtpt) REVERT: A 160 LYS cc_start: 0.9149 (tttt) cc_final: 0.8861 (tttm) REVERT: A 190 ILE cc_start: 0.8946 (mt) cc_final: 0.8581 (mm) REVERT: A 197 LEU cc_start: 0.7291 (tt) cc_final: 0.7079 (mp) REVERT: A 443 ILE cc_start: 0.7500 (tt) cc_final: 0.7198 (tp) REVERT: B 136 GLU cc_start: 0.8048 (tp30) cc_final: 0.6993 (tt0) REVERT: B 139 LYS cc_start: 0.7959 (tptt) cc_final: 0.7314 (mtpt) REVERT: B 160 LYS cc_start: 0.9078 (tttt) cc_final: 0.8758 (tttp) REVERT: C 136 GLU cc_start: 0.7994 (tp30) cc_final: 0.6779 (tt0) REVERT: C 139 LYS cc_start: 0.7989 (tptt) cc_final: 0.7471 (mtpt) REVERT: C 160 LYS cc_start: 0.9064 (tttt) cc_final: 0.8607 (ttmm) REVERT: C 205 LYS cc_start: 0.7990 (tptt) cc_final: 0.7693 (tptm) REVERT: C 322 LEU cc_start: 0.6918 (mt) cc_final: 0.6697 (tt) REVERT: C 443 ILE cc_start: 0.7450 (tt) cc_final: 0.7199 (tp) REVERT: E 114 TRP cc_start: 0.8598 (m100) cc_final: 0.8351 (m-90) REVERT: F 114 TRP cc_start: 0.8581 (m100) cc_final: 0.8074 (m100) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1324 time to fit residues: 45.6656 Evaluate side-chains 142 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127308 restraints weight = 16851.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126593 restraints weight = 17526.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126902 restraints weight = 17096.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127164 restraints weight = 15714.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127257 restraints weight = 14423.394| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13788 Z= 0.148 Angle : 0.637 8.516 18756 Z= 0.339 Chirality : 0.048 0.200 2256 Planarity : 0.005 0.043 2361 Dihedral : 5.834 53.815 2121 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.06 % Allowed : 8.84 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.20), residues: 1728 helix: 0.16 (0.24), residues: 465 sheet: 0.13 (0.26), residues: 372 loop : -0.18 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.012 0.002 TYR A 206 PHE 0.010 0.001 PHE F 46 TRP 0.011 0.001 TRP D 52 HIS 0.004 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00320 (13758) covalent geometry : angle 0.61367 (18684) SS BOND : bond 0.00502 ( 18) SS BOND : angle 1.47353 ( 36) hydrogen bonds : bond 0.05279 ( 591) hydrogen bonds : angle 6.05825 ( 1698) link_NAG-ASN : bond 0.00365 ( 12) link_NAG-ASN : angle 3.73172 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.7289 (tp30) cc_final: 0.6758 (tt0) REVERT: A 190 ILE cc_start: 0.9265 (mt) cc_final: 0.8920 (mm) REVERT: A 213 VAL cc_start: 0.9110 (t) cc_final: 0.8883 (m) REVERT: A 238 ASN cc_start: 0.8914 (t0) cc_final: 0.8404 (t0) REVERT: B 136 GLU cc_start: 0.7386 (tp30) cc_final: 0.7051 (tt0) REVERT: B 140 ASN cc_start: 0.8883 (t0) cc_final: 0.8676 (t0) REVERT: B 190 ILE cc_start: 0.9065 (mt) cc_final: 0.8757 (mm) REVERT: B 238 ASN cc_start: 0.8815 (t0) cc_final: 0.8335 (t0) REVERT: B 411 MET cc_start: 0.6837 (ttp) cc_final: 0.6494 (ttp) REVERT: C 136 GLU cc_start: 0.7352 (tp30) cc_final: 0.6894 (tt0) REVERT: C 190 ILE cc_start: 0.9088 (mt) cc_final: 0.8807 (mm) REVERT: C 238 ASN cc_start: 0.8881 (t0) cc_final: 0.8391 (t0) outliers start: 16 outliers final: 8 residues processed: 185 average time/residue: 0.1177 time to fit residues: 31.6181 Evaluate side-chains 136 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain F residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 152 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 149 optimal weight: 0.0980 chunk 164 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.138682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129692 restraints weight = 16870.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128308 restraints weight = 27688.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.129055 restraints weight = 24798.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129328 restraints weight = 17407.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129815 restraints weight = 14824.336| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13788 Z= 0.120 Angle : 0.556 6.996 18756 Z= 0.292 Chirality : 0.046 0.194 2256 Planarity : 0.004 0.042 2361 Dihedral : 5.445 52.198 2121 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.65 % Allowed : 10.30 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.20), residues: 1728 helix: 0.46 (0.24), residues: 465 sheet: 0.16 (0.25), residues: 408 loop : -0.19 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 44 TYR 0.010 0.001 TYR A 344 PHE 0.009 0.001 PHE B 376 TRP 0.009 0.001 TRP F 52 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00260 (13758) covalent geometry : angle 0.53893 (18684) SS BOND : bond 0.00315 ( 18) SS BOND : angle 1.33356 ( 36) hydrogen bonds : bond 0.04296 ( 591) hydrogen bonds : angle 5.46633 ( 1698) link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 2.93091 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.533 Fit side-chains REVERT: A 136 GLU cc_start: 0.7308 (tp30) cc_final: 0.6705 (tt0) REVERT: A 190 ILE cc_start: 0.9234 (mt) cc_final: 0.8927 (mm) REVERT: A 336 ARG cc_start: 0.7432 (mmm160) cc_final: 0.7152 (tpt170) REVERT: A 411 MET cc_start: 0.6851 (ttp) cc_final: 0.6545 (ttp) REVERT: B 190 ILE cc_start: 0.8927 (mt) cc_final: 0.8638 (mm) REVERT: B 411 MET cc_start: 0.6833 (ttp) cc_final: 0.6488 (ttp) REVERT: C 136 GLU cc_start: 0.7384 (tp30) cc_final: 0.6829 (tt0) REVERT: C 190 ILE cc_start: 0.9010 (mt) cc_final: 0.8744 (mm) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 0.1325 time to fit residues: 30.4857 Evaluate side-chains 141 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 135 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123101 restraints weight = 17226.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122381 restraints weight = 27495.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121455 restraints weight = 24426.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121153 restraints weight = 16260.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121451 restraints weight = 14681.282| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13788 Z= 0.224 Angle : 0.666 9.047 18756 Z= 0.346 Chirality : 0.050 0.194 2256 Planarity : 0.005 0.044 2361 Dihedral : 5.734 52.158 2121 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 11.29 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.20), residues: 1728 helix: 0.05 (0.24), residues: 465 sheet: -0.06 (0.25), residues: 372 loop : -0.50 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 336 TYR 0.015 0.002 TYR E 94 PHE 0.015 0.002 PHE F 46 TRP 0.017 0.002 TRP D 114 HIS 0.004 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00560 (13758) covalent geometry : angle 0.65127 (18684) SS BOND : bond 0.00239 ( 18) SS BOND : angle 1.56627 ( 36) hydrogen bonds : bond 0.04997 ( 591) hydrogen bonds : angle 5.55928 ( 1698) link_NAG-ASN : bond 0.00544 ( 12) link_NAG-ASN : angle 2.95987 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.559 Fit side-chains REVERT: A 136 GLU cc_start: 0.7432 (tp30) cc_final: 0.6739 (tt0) REVERT: A 190 ILE cc_start: 0.9238 (mt) cc_final: 0.8971 (mm) REVERT: A 336 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7246 (tpt170) REVERT: A 352 MET cc_start: 0.9064 (tpt) cc_final: 0.8740 (tpp) REVERT: B 190 ILE cc_start: 0.8952 (mt) cc_final: 0.8640 (mm) REVERT: B 218 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 411 MET cc_start: 0.7046 (ttp) cc_final: 0.6669 (ttp) REVERT: C 136 GLU cc_start: 0.7524 (tp30) cc_final: 0.6796 (tt0) REVERT: C 190 ILE cc_start: 0.9023 (mt) cc_final: 0.8718 (mm) outliers start: 41 outliers final: 26 residues processed: 153 average time/residue: 0.1311 time to fit residues: 28.9187 Evaluate side-chains 144 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 44 optimal weight: 0.8980 chunk 130 optimal weight: 0.0030 chunk 78 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125086 restraints weight = 17003.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124471 restraints weight = 17307.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124884 restraints weight = 17025.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125194 restraints weight = 15382.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125297 restraints weight = 14143.893| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13788 Z= 0.123 Angle : 0.541 7.609 18756 Z= 0.283 Chirality : 0.046 0.178 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.358 52.947 2121 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.72 % Allowed : 13.40 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1728 helix: 0.43 (0.25), residues: 465 sheet: -0.09 (0.24), residues: 408 loop : -0.44 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 353 TYR 0.009 0.001 TYR A 292 PHE 0.011 0.001 PHE B 376 TRP 0.010 0.001 TRP D 114 HIS 0.004 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00290 (13758) covalent geometry : angle 0.52763 (18684) SS BOND : bond 0.00166 ( 18) SS BOND : angle 1.20224 ( 36) hydrogen bonds : bond 0.03993 ( 591) hydrogen bonds : angle 5.12196 ( 1698) link_NAG-ASN : bond 0.00447 ( 12) link_NAG-ASN : angle 2.61217 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.512 Fit side-chains REVERT: A 190 ILE cc_start: 0.9128 (mt) cc_final: 0.8808 (mm) REVERT: A 319 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7568 (mtm180) REVERT: A 336 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7193 (tpt170) REVERT: A 411 MET cc_start: 0.6813 (ttp) cc_final: 0.6582 (ttp) REVERT: B 190 ILE cc_start: 0.8800 (mt) cc_final: 0.8540 (mm) REVERT: B 218 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8399 (tt) REVERT: B 411 MET cc_start: 0.6859 (ttp) cc_final: 0.6572 (ttp) REVERT: C 136 GLU cc_start: 0.7428 (tp30) cc_final: 0.6791 (tt0) REVERT: C 190 ILE cc_start: 0.8953 (mt) cc_final: 0.8693 (mm) REVERT: C 218 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8418 (tt) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.1300 time to fit residues: 26.2100 Evaluate side-chains 137 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 124 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121083 restraints weight = 17227.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120169 restraints weight = 24314.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120638 restraints weight = 21705.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121139 restraints weight = 18808.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121182 restraints weight = 16759.322| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13788 Z= 0.161 Angle : 0.579 8.920 18756 Z= 0.301 Chirality : 0.047 0.181 2256 Planarity : 0.004 0.045 2361 Dihedral : 5.424 53.000 2121 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.31 % Allowed : 13.40 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.20), residues: 1728 helix: 0.40 (0.25), residues: 465 sheet: -0.25 (0.25), residues: 378 loop : -0.58 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.012 0.002 TYR A 292 PHE 0.010 0.001 PHE A 376 TRP 0.013 0.002 TRP D 114 HIS 0.004 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00395 (13758) covalent geometry : angle 0.56503 (18684) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.23092 ( 36) hydrogen bonds : bond 0.04318 ( 591) hydrogen bonds : angle 5.18883 ( 1698) link_NAG-ASN : bond 0.00405 ( 12) link_NAG-ASN : angle 2.68115 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.464 Fit side-chains REVERT: A 190 ILE cc_start: 0.9142 (mt) cc_final: 0.8811 (mm) REVERT: A 336 ARG cc_start: 0.7603 (mmm160) cc_final: 0.7162 (tpt170) REVERT: B 190 ILE cc_start: 0.8816 (mt) cc_final: 0.8576 (mm) REVERT: B 218 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 411 MET cc_start: 0.6965 (ttp) cc_final: 0.6652 (ttp) REVERT: C 136 GLU cc_start: 0.7424 (tp30) cc_final: 0.6802 (tt0) REVERT: C 190 ILE cc_start: 0.8935 (mt) cc_final: 0.8665 (mm) outliers start: 35 outliers final: 26 residues processed: 147 average time/residue: 0.1236 time to fit residues: 26.7263 Evaluate side-chains 142 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141588 restraints weight = 16154.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141766 restraints weight = 15652.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142329 restraints weight = 14172.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142898 restraints weight = 12160.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143101 restraints weight = 10469.863| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13788 Z= 0.102 Angle : 0.508 9.740 18756 Z= 0.264 Chirality : 0.044 0.170 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.093 53.209 2121 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.78 % Allowed : 14.72 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1728 helix: 0.80 (0.26), residues: 447 sheet: -0.10 (0.24), residues: 450 loop : -0.56 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.007 0.001 TYR C 292 PHE 0.010 0.001 PHE B 376 TRP 0.007 0.001 TRP D 114 HIS 0.003 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00226 (13758) covalent geometry : angle 0.49518 (18684) SS BOND : bond 0.00183 ( 18) SS BOND : angle 1.12314 ( 36) hydrogen bonds : bond 0.03570 ( 591) hydrogen bonds : angle 4.91364 ( 1698) link_NAG-ASN : bond 0.00388 ( 12) link_NAG-ASN : angle 2.41031 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.444 Fit side-chains REVERT: A 190 ILE cc_start: 0.9010 (mt) cc_final: 0.8731 (mm) REVERT: A 336 ARG cc_start: 0.7541 (mmm160) cc_final: 0.7139 (tpt170) REVERT: A 463 MET cc_start: 0.7952 (ttm) cc_final: 0.7499 (ttm) REVERT: B 155 ASN cc_start: 0.8397 (p0) cc_final: 0.8159 (p0) REVERT: B 218 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 136 GLU cc_start: 0.7496 (tp30) cc_final: 0.6789 (tt0) REVERT: C 190 ILE cc_start: 0.8858 (mt) cc_final: 0.8606 (mm) REVERT: D 33 MET cc_start: 0.7348 (mmm) cc_final: 0.7117 (mtp) REVERT: E 82 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6966 (mtp) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.1197 time to fit residues: 25.8108 Evaluate side-chains 142 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 37 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128743 restraints weight = 16717.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127503 restraints weight = 29682.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127595 restraints weight = 25444.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127650 restraints weight = 21601.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127811 restraints weight = 18177.479| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13788 Z= 0.118 Angle : 0.522 9.517 18756 Z= 0.271 Chirality : 0.045 0.173 2256 Planarity : 0.004 0.042 2361 Dihedral : 5.084 53.159 2121 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.85 % Allowed : 15.12 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1728 helix: 0.83 (0.26), residues: 447 sheet: -0.13 (0.24), residues: 450 loop : -0.58 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.009 0.001 TYR B 292 PHE 0.010 0.001 PHE A 376 TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00279 (13758) covalent geometry : angle 0.50968 (18684) SS BOND : bond 0.00168 ( 18) SS BOND : angle 1.15769 ( 36) hydrogen bonds : bond 0.03691 ( 591) hydrogen bonds : angle 4.89099 ( 1698) link_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 2.42072 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.577 Fit side-chains REVERT: A 68 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.6841 (ppp) REVERT: A 190 ILE cc_start: 0.9104 (mt) cc_final: 0.8822 (mm) REVERT: A 336 ARG cc_start: 0.7524 (mmm160) cc_final: 0.7136 (tpt170) REVERT: B 218 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8407 (tt) REVERT: C 68 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.6622 (ppp) REVERT: C 136 GLU cc_start: 0.7363 (tp30) cc_final: 0.6769 (tt0) REVERT: C 190 ILE cc_start: 0.8904 (mt) cc_final: 0.8650 (mm) REVERT: D 33 MET cc_start: 0.7330 (mmm) cc_final: 0.7084 (mtp) outliers start: 28 outliers final: 24 residues processed: 144 average time/residue: 0.1226 time to fit residues: 26.1702 Evaluate side-chains 150 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123054 restraints weight = 17048.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122603 restraints weight = 21641.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123437 restraints weight = 20217.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123831 restraints weight = 16394.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124100 restraints weight = 14304.282| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13788 Z= 0.145 Angle : 0.553 10.522 18756 Z= 0.287 Chirality : 0.046 0.177 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.196 53.177 2121 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.98 % Allowed : 15.12 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1728 helix: 0.66 (0.26), residues: 465 sheet: -0.12 (0.25), residues: 387 loop : -0.59 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.011 0.001 TYR C 292 PHE 0.010 0.001 PHE B 376 TRP 0.011 0.001 TRP D 114 HIS 0.004 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00354 (13758) covalent geometry : angle 0.53969 (18684) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.25126 ( 36) hydrogen bonds : bond 0.04010 ( 591) hydrogen bonds : angle 4.98154 ( 1698) link_NAG-ASN : bond 0.00389 ( 12) link_NAG-ASN : angle 2.51511 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.543 Fit side-chains REVERT: A 68 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.6899 (ppp) REVERT: A 190 ILE cc_start: 0.9138 (mt) cc_final: 0.8852 (mm) REVERT: A 336 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7189 (tpt170) REVERT: B 68 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7436 (ppp) REVERT: B 218 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8417 (tt) REVERT: B 411 MET cc_start: 0.6896 (ttp) cc_final: 0.6635 (ttp) REVERT: C 68 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.6718 (ppp) REVERT: C 136 GLU cc_start: 0.7515 (tp30) cc_final: 0.6838 (tt0) REVERT: C 190 ILE cc_start: 0.8929 (mt) cc_final: 0.8677 (mm) REVERT: C 238 ASN cc_start: 0.8805 (t0) cc_final: 0.8459 (t0) REVERT: D 33 MET cc_start: 0.7451 (mmm) cc_final: 0.7200 (mtp) outliers start: 30 outliers final: 25 residues processed: 144 average time/residue: 0.1156 time to fit residues: 25.1916 Evaluate side-chains 150 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129950 restraints weight = 16715.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128928 restraints weight = 28209.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129262 restraints weight = 25217.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129153 restraints weight = 20415.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129586 restraints weight = 16858.414| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13788 Z= 0.104 Angle : 0.514 11.581 18756 Z= 0.265 Chirality : 0.045 0.171 2256 Planarity : 0.004 0.044 2361 Dihedral : 5.000 53.304 2121 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 15.18 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1728 helix: 0.89 (0.26), residues: 447 sheet: -0.14 (0.24), residues: 450 loop : -0.60 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.008 0.001 TYR A 135 PHE 0.010 0.001 PHE A 376 TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS D 58 Details of bonding type rmsd covalent geometry : bond 0.00236 (13758) covalent geometry : angle 0.50073 (18684) SS BOND : bond 0.00183 ( 18) SS BOND : angle 1.29815 ( 36) hydrogen bonds : bond 0.03554 ( 591) hydrogen bonds : angle 4.82731 ( 1698) link_NAG-ASN : bond 0.00386 ( 12) link_NAG-ASN : angle 2.36252 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.550 Fit side-chains REVERT: A 68 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.6745 (ppp) REVERT: A 190 ILE cc_start: 0.9076 (mt) cc_final: 0.8819 (mm) REVERT: A 336 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7101 (tpt170) REVERT: A 463 MET cc_start: 0.7843 (ttm) cc_final: 0.7634 (ttm) REVERT: B 68 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7386 (ppp) REVERT: B 218 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 68 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6558 (ppp) REVERT: C 136 GLU cc_start: 0.7414 (tp30) cc_final: 0.6810 (tt0) REVERT: C 190 ILE cc_start: 0.8867 (mt) cc_final: 0.8639 (mm) outliers start: 32 outliers final: 25 residues processed: 146 average time/residue: 0.1138 time to fit residues: 25.1187 Evaluate side-chains 150 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 167 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128609 restraints weight = 17038.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127627 restraints weight = 28594.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127278 restraints weight = 24988.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126855 restraints weight = 25143.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127424 restraints weight = 19549.400| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13788 Z= 0.115 Angle : 0.529 12.826 18756 Z= 0.272 Chirality : 0.045 0.172 2256 Planarity : 0.004 0.043 2361 Dihedral : 5.004 53.218 2121 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.11 % Allowed : 15.31 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1728 helix: 0.82 (0.26), residues: 450 sheet: -0.09 (0.24), residues: 417 loop : -0.65 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.009 0.001 TYR A 292 PHE 0.010 0.001 PHE A 376 TRP 0.009 0.001 TRP D 114 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00269 (13758) covalent geometry : angle 0.51662 (18684) SS BOND : bond 0.00195 ( 18) SS BOND : angle 1.26174 ( 36) hydrogen bonds : bond 0.03639 ( 591) hydrogen bonds : angle 4.84371 ( 1698) link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 2.36401 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.61 seconds wall clock time: 38 minutes 0.43 seconds (2280.43 seconds total)