Starting phenix.real_space_refine on Fri Sep 11 17:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2q_26318/09_2026/7u2q_26318.map" } resolution = 3.2 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= 0.008 sd= 0.143 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 84 5.16 5 C 6656 2.51 5 N 1780 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2606 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 2.43, per 1000 atoms: 0.23 Number of scatterers: 10536 At special positions: 0 Unit cell: (119.48, 119.48, 64.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2016 8.00 N 1780 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.07 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.07 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.03 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 88 " " NAG A 502 " - " ASN A 235 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 235 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 235 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 235 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 396.6 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 3.3% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS A 111 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS B 111 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS C 111 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.893A pdb=" N LYS D 111 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER A 444 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 402 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY A 395 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU A 158 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA A 232 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG A 257 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS A 279 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 291 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS A 281 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 289 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER B 444 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR B 402 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY B 395 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU B 158 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA B 232 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG B 257 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS B 279 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 291 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS B 281 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 289 " --> pdb=" O CYS B 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER C 444 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR C 402 " --> pdb=" O GLU C 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY C 395 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU C 158 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA C 232 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS C 279 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL C 291 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS C 281 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR C 289 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 103 removed outlier: 6.752A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR D 402 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY D 395 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 121 through 124 removed outlier: 6.791A pdb=" N LEU D 158 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.516A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.645A pdb=" N ALA D 232 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 224 through 225 removed outlier: 7.129A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG D 257 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 277 through 284 removed outlier: 4.891A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 936 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: 1.76 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2658 1.33 - 1.46: 3154 1.46 - 1.60: 4892 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 10808 Sorted by residual: bond pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU A 119 " pdb=" CA GLU A 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N GLU D 119 " pdb=" CA GLU D 119 " ideal model delta sigma weight residual 1.458 1.497 -0.040 7.40e-03 1.83e+04 2.87e+01 bond pdb=" N VAL D 106 " pdb=" CA VAL D 106 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 ... (remaining 10803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11062 1.53 - 3.07: 2778 3.07 - 4.60: 640 4.60 - 6.14: 153 6.14 - 7.67: 43 Bond angle restraints: 14676 Sorted by residual: angle pdb=" C GLY B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY A 197 " pdb=" N PRO A 198 " pdb=" CA PRO A 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C GLY D 197 " pdb=" N PRO D 198 " pdb=" CA PRO D 198 " ideal model delta sigma weight residual 119.85 127.52 -7.67 1.01e+00 9.80e-01 5.77e+01 angle pdb=" C ASP D 376 " pdb=" N PRO D 377 " pdb=" CA PRO D 377 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.01e+00 9.80e-01 4.79e+01 ... (remaining 14671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 5843 16.01 - 32.02: 305 32.02 - 48.03: 84 48.03 - 64.05: 48 64.05 - 80.06: 8 Dihedral angle restraints: 6288 sinusoidal: 2472 harmonic: 3816 Sorted by residual: dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 335 " pdb=" CB CYS B 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 dihedral pdb=" CB CYS C 318 " pdb=" SG CYS C 318 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 119.03 -26.03 1 1.00e+01 1.00e-02 9.74e+00 ... (remaining 6285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 925 0.068 - 0.135: 456 0.135 - 0.203: 137 0.203 - 0.270: 54 0.270 - 0.338: 16 Chirality restraints: 1588 Sorted by residual: chirality pdb=" CB VAL D 83 " pdb=" CA VAL D 83 " pdb=" CG1 VAL D 83 " pdb=" CG2 VAL D 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL C 83 " pdb=" CA VAL C 83 " pdb=" CG1 VAL C 83 " pdb=" CG2 VAL C 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL A 83 " pdb=" CA VAL A 83 " pdb=" CG1 VAL A 83 " pdb=" CG2 VAL A 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.97 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1585 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG A 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG B 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.046 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG C 502 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.060 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.008 2.00e-02 2.50e+03 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5584 3.00 - 3.47: 9443 3.47 - 3.95: 17936 3.95 - 4.42: 21194 4.42 - 4.90: 34347 Nonbonded interactions: 88504 Sorted by model distance: nonbonded pdb=" N ASP B 416 " pdb=" OD1 ASP B 416 " model vdw 2.525 3.120 nonbonded pdb=" N ASP A 416 " pdb=" OD1 ASP A 416 " model vdw 2.525 3.120 nonbonded pdb=" N ASP D 416 " pdb=" OD1 ASP D 416 " model vdw 2.525 3.120 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.525 3.120 nonbonded pdb=" N SER D 125 " pdb=" O SER D 125 " model vdw 2.534 2.496 ... (remaining 88499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.014 0.072 10848 Z= 0.825 Angle : 1.534 10.035 14764 Z= 1.078 Chirality : 0.094 0.338 1588 Planarity : 0.006 0.038 1868 Dihedral : 12.316 80.057 3752 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.96 % Favored : 95.73 % Rotamer: Outliers : 4.83 % Allowed : 2.76 % Favored : 92.41 % 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 are not related in a simple way. whole: -0.35 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.19 (0.24), residues: 456 loop : -0.44 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 225 TYR 0.038 0.007 TYR D 276 PHE 0.019 0.004 PHE B 406 TRP 0.019 0.003 TRP D 179 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.01349 / 0.82 (10808) covalent geometry : angle 1.51862 / 1.07 (14676) SS BOND : bond 0.01370 / 0.91 ( 32) SS BOND : angle 3.57937 / 2.28 ( 64) hydrogen bonds : bond 0.17420 / 12.08 ( 360) hydrogen bonds : angle 9.02785 / 6.35 ( 936) link_NAG-ASN : bond 0.04454 / 2.32 ( 8) link_NAG-ASN : angle 1.92144 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 0.422 Fit side-chains REVERT: A 159 MET cc_start: 0.8596 (mtp) cc_final: 0.8376 (mtt) REVERT: A 226 THR cc_start: 0.9115 (t) cc_final: 0.8903 (t) REVERT: B 159 MET cc_start: 0.8597 (mtp) cc_final: 0.8377 (mtt) REVERT: B 226 THR cc_start: 0.9108 (t) cc_final: 0.8895 (t) REVERT: C 159 MET cc_start: 0.8589 (mtp) cc_final: 0.8372 (mtt) REVERT: C 226 THR cc_start: 0.9116 (t) cc_final: 0.8903 (t) REVERT: D 159 MET cc_start: 0.8587 (mtp) cc_final: 0.8371 (mtt) REVERT: D 226 THR cc_start: 0.9113 (t) cc_final: 0.8896 (t) outliers start: 56 outliers final: 0 residues processed: 348 average time/residue: 0.1057 time to fit residues: 51.9108 Evaluate side-chains 140 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN A 369 ASN B 189 ASN B 369 ASN C 189 ASN C 369 ASN D 189 ASN D 369 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124344 restraints weight = 11916.551| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.38 r_work: 0.3319 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10848 Z= 0.121 Angle : 0.580 5.056 14764 Z= 0.315 Chirality : 0.048 0.133 1588 Planarity : 0.005 0.037 1868 Dihedral : 4.912 16.213 1432 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 2.33 % Allowed : 8.62 % Favored : 89.05 % 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 are not related in a simple way. whole: 0.01 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.23 (0.20), residues: 516 loop : -0.06 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 156 TYR 0.011 0.001 TYR A 253 PHE 0.018 0.002 PHE D 406 TRP 0.014 0.002 TRP B 179 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10808) covalent geometry : angle 0.57391 / 0.31 (14676) SS BOND : bond 0.00173 / 0.11 ( 32) SS BOND : angle 1.17150 / 0.78 ( 64) hydrogen bonds : bond 0.03545 / 2.51 ( 360) hydrogen bonds : angle 6.91506 / 4.87 ( 936) link_NAG-ASN : bond 0.00352 / 0.19 ( 8) link_NAG-ASN : angle 1.42116 / 0.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.352 Fit side-chains REVERT: A 189 ASN cc_start: 0.8816 (m110) cc_final: 0.8470 (m110) REVERT: A 226 THR cc_start: 0.9220 (t) cc_final: 0.8956 (t) REVERT: A 231 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7377 (p) REVERT: A 314 ILE cc_start: 0.8941 (pt) cc_final: 0.8521 (mt) REVERT: A 368 ARG cc_start: 0.8023 (mmp80) cc_final: 0.7784 (mmp80) REVERT: B 189 ASN cc_start: 0.8840 (m110) cc_final: 0.8497 (m110) REVERT: B 226 THR cc_start: 0.9211 (t) cc_final: 0.8948 (t) REVERT: B 231 CYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7353 (p) REVERT: B 268 GLU cc_start: 0.7697 (tt0) cc_final: 0.7415 (tt0) REVERT: B 314 ILE cc_start: 0.8941 (pt) cc_final: 0.8521 (mt) REVERT: B 368 ARG cc_start: 0.8036 (mmp80) cc_final: 0.7794 (mmp80) REVERT: B 428 ARG cc_start: 0.6918 (mmt90) cc_final: 0.6709 (mmt90) REVERT: C 189 ASN cc_start: 0.8820 (m110) cc_final: 0.8479 (m110) REVERT: C 200 ASN cc_start: 0.7987 (t0) cc_final: 0.7779 (t0) REVERT: C 226 THR cc_start: 0.9223 (t) cc_final: 0.8958 (t) REVERT: C 231 CYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7357 (p) REVERT: C 314 ILE cc_start: 0.8948 (pt) cc_final: 0.8536 (mt) REVERT: C 368 ARG cc_start: 0.8040 (mmp80) cc_final: 0.7795 (mmp80) REVERT: C 428 ARG cc_start: 0.6881 (mmt90) cc_final: 0.6666 (mmt90) REVERT: D 189 ASN cc_start: 0.8835 (m110) cc_final: 0.8492 (m110) REVERT: D 226 THR cc_start: 0.9213 (t) cc_final: 0.8945 (t) REVERT: D 231 CYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7367 (p) REVERT: D 314 ILE cc_start: 0.8947 (pt) cc_final: 0.8535 (mt) REVERT: D 368 ARG cc_start: 0.8032 (mmp80) cc_final: 0.7789 (mmp80) REVERT: D 428 ARG cc_start: 0.6871 (mmt90) cc_final: 0.6662 (mmt90) outliers start: 27 outliers final: 15 residues processed: 205 average time/residue: 0.1057 time to fit residues: 30.7651 Evaluate side-chains 192 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN A 222 ASN B 222 ASN C 222 ASN D 200 ASN D 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124943 restraints weight = 11925.142| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.37 r_work: 0.3218 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10848 Z= 0.145 Angle : 0.530 4.758 14764 Z= 0.286 Chirality : 0.048 0.141 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.586 16.678 1432 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.44 % Favored : 97.26 % Rotamer: Outliers : 2.93 % Allowed : 8.79 % Favored : 88.28 % 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 are not related in a simple way. whole: -0.08 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.20 (0.20), residues: 544 loop : -0.16 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 428 TYR 0.008 0.001 TYR A 253 PHE 0.017 0.002 PHE B 406 TRP 0.013 0.001 TRP B 179 HIS 0.005 0.002 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (10808) covalent geometry : angle 0.52548 / 0.28 (14676) SS BOND : bond 0.00180 / 0.11 ( 32) SS BOND : angle 1.02524 / 0.68 ( 64) hydrogen bonds : bond 0.03170 / 2.22 ( 360) hydrogen bonds : angle 6.58042 / 4.66 ( 936) link_NAG-ASN : bond 0.00223 / 0.12 ( 8) link_NAG-ASN : angle 1.14853 / 0.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9201 (p) cc_final: 0.8852 (t) REVERT: A 189 ASN cc_start: 0.8894 (m110) cc_final: 0.8604 (m110) REVERT: A 287 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 314 ILE cc_start: 0.9024 (pt) cc_final: 0.8572 (mt) REVERT: A 428 ARG cc_start: 0.7002 (mmt90) cc_final: 0.6685 (mmt90) REVERT: B 89 SER cc_start: 0.9207 (p) cc_final: 0.8855 (t) REVERT: B 189 ASN cc_start: 0.8915 (m110) cc_final: 0.8630 (m110) REVERT: B 200 ASN cc_start: 0.8157 (t0) cc_final: 0.7861 (t0) REVERT: B 268 GLU cc_start: 0.7853 (tt0) cc_final: 0.7615 (tt0) REVERT: B 287 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: B 314 ILE cc_start: 0.9038 (pt) cc_final: 0.8592 (mt) REVERT: B 428 ARG cc_start: 0.7207 (mmt90) cc_final: 0.6963 (mmt90) REVERT: C 89 SER cc_start: 0.9203 (p) cc_final: 0.8866 (t) REVERT: C 189 ASN cc_start: 0.8907 (m110) cc_final: 0.8599 (m110) REVERT: C 200 ASN cc_start: 0.8143 (t0) cc_final: 0.7934 (t0) REVERT: C 287 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: C 314 ILE cc_start: 0.9034 (pt) cc_final: 0.8585 (mt) REVERT: C 428 ARG cc_start: 0.7202 (mmt90) cc_final: 0.6955 (mmt90) REVERT: D 89 SER cc_start: 0.9198 (p) cc_final: 0.8847 (t) REVERT: D 189 ASN cc_start: 0.8943 (m110) cc_final: 0.8633 (m-40) REVERT: D 287 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: D 314 ILE cc_start: 0.9045 (pt) cc_final: 0.8599 (mt) outliers start: 34 outliers final: 19 residues processed: 196 average time/residue: 0.1058 time to fit residues: 29.0557 Evaluate side-chains 179 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 313 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN C 227 GLN D 200 ASN D 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113910 restraints weight = 12486.844| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.63 r_work: 0.3129 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10848 Z= 0.124 Angle : 0.498 4.831 14764 Z= 0.266 Chirality : 0.047 0.132 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.431 17.067 1432 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.83 % Favored : 97.87 % Rotamer: Outliers : 2.24 % Allowed : 11.72 % Favored : 86.03 % 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 are not related in a simple way. whole: -0.20 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.08 (0.20), residues: 548 loop : -0.20 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 428 TYR 0.006 0.001 TYR B 253 PHE 0.017 0.002 PHE D 406 TRP 0.012 0.001 TRP B 179 HIS 0.005 0.002 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 (10808) covalent geometry : angle 0.49396 / 0.27 (14676) SS BOND : bond 0.00193 / 0.12 ( 32) SS BOND : angle 0.94873 / 0.63 ( 64) hydrogen bonds : bond 0.02746 / 1.95 ( 360) hydrogen bonds : angle 6.27427 / 4.44 ( 936) link_NAG-ASN : bond 0.00192 / 0.10 ( 8) link_NAG-ASN : angle 1.09176 / 0.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9247 (p) cc_final: 0.8945 (t) REVERT: A 170 TYR cc_start: 0.8797 (m-80) cc_final: 0.8579 (m-10) REVERT: A 189 ASN cc_start: 0.9043 (m110) cc_final: 0.8723 (m110) REVERT: A 222 ASN cc_start: 0.7905 (t0) cc_final: 0.7507 (t0) REVERT: A 311 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7620 (mm-30) REVERT: A 428 ARG cc_start: 0.7094 (mmt90) cc_final: 0.6846 (mmt90) REVERT: B 89 SER cc_start: 0.9250 (p) cc_final: 0.8949 (t) REVERT: B 170 TYR cc_start: 0.8790 (m-80) cc_final: 0.8575 (m-10) REVERT: B 189 ASN cc_start: 0.9063 (m110) cc_final: 0.8744 (m110) REVERT: B 222 ASN cc_start: 0.7913 (t0) cc_final: 0.7524 (t0) REVERT: B 311 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7707 (mm-30) REVERT: B 368 ARG cc_start: 0.7920 (mmp80) cc_final: 0.7565 (mmp80) REVERT: C 89 SER cc_start: 0.9173 (p) cc_final: 0.8856 (t) REVERT: C 170 TYR cc_start: 0.8781 (m-80) cc_final: 0.8569 (m-10) REVERT: C 189 ASN cc_start: 0.9071 (m110) cc_final: 0.8651 (m-40) REVERT: D 89 SER cc_start: 0.9244 (p) cc_final: 0.8941 (t) REVERT: D 170 TYR cc_start: 0.8795 (m-80) cc_final: 0.8586 (m-10) REVERT: D 189 ASN cc_start: 0.9053 (m110) cc_final: 0.8721 (m-40) REVERT: D 368 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7581 (mmp80) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.1061 time to fit residues: 27.2993 Evaluate side-chains 163 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117499 restraints weight = 12307.029| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.57 r_work: 0.3187 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10848 Z= 0.099 Angle : 0.480 5.302 14764 Z= 0.257 Chirality : 0.047 0.132 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.284 17.452 1432 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 11.72 % Favored : 86.38 % 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 are not related in a simple way. whole: -0.06 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.21 (0.20), residues: 568 loop : -0.14 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 428 TYR 0.007 0.001 TYR C 274 PHE 0.014 0.002 PHE D 406 TRP 0.010 0.001 TRP B 179 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10808) covalent geometry : angle 0.47672 / 0.26 (14676) SS BOND : bond 0.00188 / 0.11 ( 32) SS BOND : angle 0.84998 / 0.56 ( 64) hydrogen bonds : bond 0.02679 / 1.88 ( 360) hydrogen bonds : angle 6.08206 / 4.30 ( 936) link_NAG-ASN : bond 0.00183 / 0.10 ( 8) link_NAG-ASN : angle 1.02093 / 0.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9183 (p) cc_final: 0.8870 (t) REVERT: A 189 ASN cc_start: 0.9072 (m110) cc_final: 0.8742 (m-40) REVERT: A 311 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7688 (mm-30) REVERT: A 368 ARG cc_start: 0.7944 (mmp80) cc_final: 0.7559 (mmp80) REVERT: A 428 ARG cc_start: 0.7099 (mmt90) cc_final: 0.6883 (mmt90) REVERT: B 89 SER cc_start: 0.9184 (p) cc_final: 0.8873 (t) REVERT: B 189 ASN cc_start: 0.9090 (m110) cc_final: 0.8767 (m-40) REVERT: B 311 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7759 (mm-30) REVERT: B 368 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7560 (mmp80) REVERT: C 89 SER cc_start: 0.9175 (p) cc_final: 0.8874 (t) REVERT: C 189 ASN cc_start: 0.9051 (m110) cc_final: 0.8776 (m-40) REVERT: C 311 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7762 (mm-30) REVERT: C 368 ARG cc_start: 0.7960 (mmp80) cc_final: 0.7571 (mmp80) REVERT: D 89 SER cc_start: 0.9184 (p) cc_final: 0.8872 (t) REVERT: D 189 ASN cc_start: 0.9080 (m110) cc_final: 0.8746 (m-40) REVERT: D 368 ARG cc_start: 0.7936 (mmp80) cc_final: 0.7571 (mmp80) outliers start: 22 outliers final: 19 residues processed: 172 average time/residue: 0.1050 time to fit residues: 25.9662 Evaluate side-chains 176 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110645 restraints weight = 12548.024| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.70 r_work: 0.3116 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10848 Z= 0.151 Angle : 0.510 5.748 14764 Z= 0.272 Chirality : 0.048 0.131 1588 Planarity : 0.004 0.045 1868 Dihedral : 4.368 16.797 1432 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.45 % Favored : 98.25 % Rotamer: Outliers : 2.67 % Allowed : 11.72 % Favored : 85.60 % 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 are not related in a simple way. whole: -0.33 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.02 (0.20), residues: 576 loop : -0.30 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 428 TYR 0.008 0.001 TYR B 276 PHE 0.018 0.002 PHE A 406 TRP 0.011 0.001 TRP A 179 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (10808) covalent geometry : angle 0.50508 / 0.27 (14676) SS BOND : bond 0.00232 / 0.14 ( 32) SS BOND : angle 0.97253 / 0.64 ( 64) hydrogen bonds : bond 0.02697 / 1.92 ( 360) hydrogen bonds : angle 6.16807 / 4.35 ( 936) link_NAG-ASN : bond 0.00152 / 0.08 ( 8) link_NAG-ASN : angle 1.17312 / 0.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9196 (p) cc_final: 0.8937 (t) REVERT: A 189 ASN cc_start: 0.9102 (m110) cc_final: 0.8798 (m-40) REVERT: A 273 ASN cc_start: 0.7361 (m-40) cc_final: 0.6919 (t0) REVERT: A 311 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7690 (mm-30) REVERT: A 428 ARG cc_start: 0.7067 (mmt90) cc_final: 0.6824 (mmt90) REVERT: B 89 SER cc_start: 0.9198 (p) cc_final: 0.8940 (t) REVERT: B 273 ASN cc_start: 0.7328 (m-40) cc_final: 0.6961 (t0) REVERT: B 311 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7664 (mm-30) REVERT: B 428 ARG cc_start: 0.6961 (mmt90) cc_final: 0.6611 (mmt90) REVERT: C 89 SER cc_start: 0.9190 (p) cc_final: 0.8946 (t) REVERT: C 189 ASN cc_start: 0.9128 (m110) cc_final: 0.8791 (m-40) REVERT: C 273 ASN cc_start: 0.7343 (m-40) cc_final: 0.6927 (t0) REVERT: C 311 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7675 (mm-30) REVERT: C 428 ARG cc_start: 0.6939 (mmt90) cc_final: 0.6582 (mmt90) REVERT: D 89 SER cc_start: 0.9196 (p) cc_final: 0.8941 (t) REVERT: D 189 ASN cc_start: 0.9118 (m110) cc_final: 0.8821 (m-40) REVERT: D 273 ASN cc_start: 0.7368 (m-40) cc_final: 0.6962 (t0) REVERT: D 428 ARG cc_start: 0.7015 (mmt90) cc_final: 0.6705 (mmt90) outliers start: 31 outliers final: 22 residues processed: 171 average time/residue: 0.0935 time to fit residues: 23.3138 Evaluate side-chains 159 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 376 ASP Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.0670 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115717 restraints weight = 12397.145| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.62 r_work: 0.3188 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10848 Z= 0.085 Angle : 0.471 5.663 14764 Z= 0.254 Chirality : 0.047 0.130 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.150 17.319 1432 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.12 % Allowed : 13.79 % Favored : 85.09 % 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 are not related in a simple way. whole: -0.23 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.01 (0.20), residues: 576 loop : -0.19 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 428 TYR 0.006 0.001 TYR B 253 PHE 0.015 0.002 PHE D 406 TRP 0.010 0.001 TRP C 179 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (10808) covalent geometry : angle 0.46756 / 0.25 (14676) SS BOND : bond 0.00173 / 0.10 ( 32) SS BOND : angle 0.80265 / 0.53 ( 64) hydrogen bonds : bond 0.02528 / 1.79 ( 360) hydrogen bonds : angle 5.83153 / 4.11 ( 936) link_NAG-ASN : bond 0.00192 / 0.10 ( 8) link_NAG-ASN : angle 0.98059 / 0.60 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9201 (p) cc_final: 0.8911 (t) REVERT: A 189 ASN cc_start: 0.9103 (m110) cc_final: 0.8712 (m-40) REVERT: A 311 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7680 (mm-30) REVERT: B 89 SER cc_start: 0.9204 (p) cc_final: 0.8920 (t) REVERT: B 189 ASN cc_start: 0.9120 (m110) cc_final: 0.8725 (m-40) REVERT: B 311 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7655 (mm-30) REVERT: B 428 ARG cc_start: 0.7113 (mmt90) cc_final: 0.6823 (mmt90) REVERT: C 89 SER cc_start: 0.9194 (p) cc_final: 0.8917 (t) REVERT: C 189 ASN cc_start: 0.9117 (m110) cc_final: 0.8720 (m-40) REVERT: C 311 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7702 (mm-30) REVERT: C 428 ARG cc_start: 0.7097 (mmt90) cc_final: 0.6804 (mmt90) REVERT: D 89 SER cc_start: 0.9204 (p) cc_final: 0.8916 (t) REVERT: D 189 ASN cc_start: 0.9137 (m110) cc_final: 0.8737 (m-40) REVERT: D 311 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7734 (mm-30) REVERT: D 428 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6833 (mmt90) outliers start: 13 outliers final: 13 residues processed: 157 average time/residue: 0.0986 time to fit residues: 22.7667 Evaluate side-chains 144 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 376 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 275 HIS B 227 GLN C 227 GLN D 227 GLN D 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.148146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115399 restraints weight = 12335.295| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.59 r_work: 0.3262 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10848 Z= 0.115 Angle : 0.547 12.661 14764 Z= 0.288 Chirality : 0.049 0.327 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.195 17.300 1432 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 13.19 % Favored : 84.91 % 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 are not related in a simple way. whole: -0.22 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.01 (0.20), residues: 576 loop : -0.16 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.006 0.001 TYR A 253 PHE 0.016 0.002 PHE C 406 TRP 0.007 0.001 TRP C 179 HIS 0.002 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.11 (10808) covalent geometry : angle 0.52928 / 0.28 (14676) SS BOND : bond 0.00545 / 0.42 ( 32) SS BOND : angle 2.08377 / 1.59 ( 64) hydrogen bonds : bond 0.02595 / 1.84 ( 360) hydrogen bonds : angle 5.87676 / 4.15 ( 936) link_NAG-ASN : bond 0.00147 / 0.08 ( 8) link_NAG-ASN : angle 1.05536 / 0.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9199 (p) cc_final: 0.8933 (t) REVERT: A 189 ASN cc_start: 0.9090 (m110) cc_final: 0.8795 (m-40) REVERT: A 311 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7723 (mm-30) REVERT: B 89 SER cc_start: 0.9205 (p) cc_final: 0.8942 (t) REVERT: B 311 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7662 (mm-30) REVERT: B 428 ARG cc_start: 0.7121 (mmt90) cc_final: 0.6815 (mmt90) REVERT: C 89 SER cc_start: 0.9185 (p) cc_final: 0.8926 (t) REVERT: C 128 GLU cc_start: 0.8304 (pt0) cc_final: 0.8066 (pt0) REVERT: C 189 ASN cc_start: 0.9087 (m110) cc_final: 0.8800 (m-40) REVERT: C 428 ARG cc_start: 0.7091 (mmt90) cc_final: 0.6830 (mmt90) REVERT: D 89 SER cc_start: 0.9198 (p) cc_final: 0.8925 (t) REVERT: D 189 ASN cc_start: 0.9113 (m110) cc_final: 0.8844 (m-40) REVERT: D 428 ARG cc_start: 0.7043 (mmt90) cc_final: 0.6779 (mmt90) outliers start: 22 outliers final: 16 residues processed: 159 average time/residue: 0.0984 time to fit residues: 22.7804 Evaluate side-chains 152 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN B 275 HIS C 227 GLN C 275 HIS D 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113504 restraints weight = 12420.934| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.59 r_work: 0.3229 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10848 Z= 0.149 Angle : 0.618 17.254 14764 Z= 0.322 Chirality : 0.050 0.296 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.313 17.075 1432 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 2.07 % Allowed : 12.50 % Favored : 85.43 % 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 are not related in a simple way. whole: -0.35 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.07 (0.20), residues: 576 loop : -0.27 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.007 0.001 TYR C 276 PHE 0.019 0.002 PHE A 406 TRP 0.008 0.001 TRP D 179 HIS 0.002 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.15 (10808) covalent geometry : angle 0.59807 / 0.31 (14676) SS BOND : bond 0.00922 / 0.69 ( 32) SS BOND : angle 2.34733 / 1.73 ( 64) hydrogen bonds : bond 0.02616 / 1.87 ( 360) hydrogen bonds : angle 6.04251 / 4.28 ( 936) link_NAG-ASN : bond 0.00279 / 0.16 ( 8) link_NAG-ASN : angle 1.07593 / 0.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9215 (p) cc_final: 0.8955 (t) REVERT: A 128 GLU cc_start: 0.8303 (pt0) cc_final: 0.8073 (pt0) REVERT: A 189 ASN cc_start: 0.9152 (m110) cc_final: 0.8760 (m-40) REVERT: A 287 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 311 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7775 (mm-30) REVERT: B 89 SER cc_start: 0.9184 (p) cc_final: 0.8918 (t) REVERT: B 128 GLU cc_start: 0.8302 (pt0) cc_final: 0.8080 (pt0) REVERT: B 428 ARG cc_start: 0.7103 (mmt90) cc_final: 0.6890 (mmt90) REVERT: C 89 SER cc_start: 0.9198 (p) cc_final: 0.8961 (t) REVERT: C 128 GLU cc_start: 0.8360 (pt0) cc_final: 0.8126 (pt0) REVERT: D 89 SER cc_start: 0.9213 (p) cc_final: 0.8959 (t) REVERT: D 189 ASN cc_start: 0.9152 (m110) cc_final: 0.8764 (m-40) REVERT: D 428 ARG cc_start: 0.7070 (mmt90) cc_final: 0.6809 (mmt90) outliers start: 24 outliers final: 19 residues processed: 153 average time/residue: 0.0992 time to fit residues: 22.0070 Evaluate side-chains 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 0.0170 chunk 122 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN B 227 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115654 restraints weight = 12313.108| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.57 r_work: 0.3164 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10848 Z= 0.112 Angle : 0.584 16.220 14764 Z= 0.305 Chirality : 0.049 0.218 1588 Planarity : 0.004 0.041 1868 Dihedral : 4.242 17.173 1432 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.64 % Allowed : 13.10 % Favored : 85.26 % 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 are not related in a simple way. whole: -0.23 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: 0.01 (0.20), residues: 560 loop : -0.18 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.006 0.001 TYR D 274 PHE 0.015 0.002 PHE B 406 TRP 0.009 0.001 TRP B 179 HIS 0.002 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.11 (10808) covalent geometry : angle 0.57020 / 0.30 (14676) SS BOND : bond 0.00848 / 0.62 ( 32) SS BOND : angle 1.95703 / 1.42 ( 64) hydrogen bonds : bond 0.02613 / 1.86 ( 360) hydrogen bonds : angle 5.92649 / 4.18 ( 936) link_NAG-ASN : bond 0.00349 / 0.18 ( 8) link_NAG-ASN : angle 0.91352 / 0.57 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9184 (p) cc_final: 0.8911 (t) REVERT: A 128 GLU cc_start: 0.8260 (pt0) cc_final: 0.8017 (pt0) REVERT: A 189 ASN cc_start: 0.9052 (m110) cc_final: 0.8775 (m-40) REVERT: A 287 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: A 311 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7674 (mm-30) REVERT: B 89 SER cc_start: 0.9195 (p) cc_final: 0.8928 (t) REVERT: B 128 GLU cc_start: 0.8268 (pt0) cc_final: 0.8039 (pt0) REVERT: B 268 GLU cc_start: 0.7695 (tt0) cc_final: 0.7454 (tt0) REVERT: C 89 SER cc_start: 0.9179 (p) cc_final: 0.8913 (t) REVERT: C 128 GLU cc_start: 0.8269 (pt0) cc_final: 0.8014 (pt0) REVERT: C 428 ARG cc_start: 0.7104 (mmt90) cc_final: 0.6880 (mmt90) REVERT: D 89 SER cc_start: 0.9175 (p) cc_final: 0.8907 (t) REVERT: D 189 ASN cc_start: 0.9073 (m110) cc_final: 0.8823 (m-40) REVERT: D 428 ARG cc_start: 0.7068 (mmt90) cc_final: 0.6824 (mmt90) outliers start: 19 outliers final: 18 residues processed: 156 average time/residue: 0.1006 time to fit residues: 22.8878 Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LYS Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 313 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 GLN C 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116025 restraints weight = 12456.562| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.58 r_work: 0.3166 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10848 Z= 0.116 Angle : 0.590 15.509 14764 Z= 0.309 Chirality : 0.049 0.215 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.231 16.919 1432 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.72 % Allowed : 13.19 % Favored : 85.09 % 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 are not related in a simple way. whole: -0.22 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: -0.02 (0.20), residues: 560 loop : -0.14 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 428 TYR 0.007 0.001 TYR D 274 PHE 0.016 0.002 PHE B 406 TRP 0.007 0.001 TRP D 190 HIS 0.002 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.11 (10808) covalent geometry : angle 0.57770 / 0.30 (14676) SS BOND : bond 0.00815 / 0.59 ( 32) SS BOND : angle 1.87932 / 1.36 ( 64) hydrogen bonds : bond 0.02614 / 1.88 ( 360) hydrogen bonds : angle 5.90056 / 4.16 ( 936) link_NAG-ASN : bond 0.00224 / 0.12 ( 8) link_NAG-ASN : angle 0.91807 / 0.57 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.17 seconds wall clock time: 44 minutes 33.49 seconds (2673.49 seconds total)