Starting phenix.real_space_refine on Wed Mar 4 03:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2q_26318/03_2026/7u2q_26318.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2q_26318/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2q_26318/03_2026/7u2q_26318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2q_26318/03_2026/7u2q_26318.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2q_26318/03_2026/7u2q_26318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2q_26318/03_2026/7u2q_26318.cif" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 2.07, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 547.7 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: 0.38 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: 1.67 Time building geometry restraints manager: 1.15 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: 5995 16.01 - 32.02: 321 32.02 - 48.03: 84 48.03 - 64.05: 48 64.05 - 80.06: 8 Dihedral angle restraints: 6456 sinusoidal: 2640 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 6453 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: 0.03 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: 0.600 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.510 Find NCS groups from input model: 0.080 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 12.140 80.057 3920 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 covalent geometry : bond 0.01349 (10808) covalent geometry : angle 1.51862 (14676) SS BOND : bond 0.01370 ( 32) SS BOND : angle 3.57937 ( 64) hydrogen bonds : bond 0.17420 ( 360) hydrogen bonds : angle 9.02785 ( 936) link_NAG-ASN : bond 0.04454 ( 8) link_NAG-ASN : angle 1.92144 ( 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 : 0.409 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: 0.1000 time to fit residues: 48.8264 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 : 0.284 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 369 ASN B 189 ASN B 369 ASN C 189 ASN C 369 ASN C 449 ASN D 189 ASN D 369 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122772 restraints weight = 11975.848| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.38 r_work: 0.3302 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10848 Z= 0.125 Angle : 0.583 5.125 14764 Z= 0.318 Chirality : 0.048 0.131 1588 Planarity : 0.005 0.037 1868 Dihedral : 4.888 16.087 1600 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 2.33 % Allowed : 8.71 % Favored : 88.97 % 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: 0.24 (0.20), residues: 516 loop : -0.07 (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 0.020 0.002 PHE D 406 TRP 0.014 0.001 TRP B 179 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00284 (10808) covalent geometry : angle 0.57723 (14676) SS BOND : bond 0.00225 ( 32) SS BOND : angle 1.19170 ( 64) hydrogen bonds : bond 0.03640 ( 360) hydrogen bonds : angle 6.92958 ( 936) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 1.25885 ( 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 : 0.327 Fit side-chains REVERT: A 189 ASN cc_start: 0.8788 (m110) cc_final: 0.8437 (m110) REVERT: A 226 THR cc_start: 0.9198 (t) cc_final: 0.8933 (t) REVERT: A 231 CYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7302 (p) REVERT: A 314 ILE cc_start: 0.8937 (pt) cc_final: 0.8499 (mt) REVERT: B 189 ASN cc_start: 0.8812 (m110) cc_final: 0.8463 (m110) REVERT: B 226 THR cc_start: 0.9189 (t) cc_final: 0.8925 (t) REVERT: B 231 CYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7282 (p) REVERT: B 268 GLU cc_start: 0.7716 (tt0) cc_final: 0.7434 (tt0) REVERT: B 314 ILE cc_start: 0.8936 (pt) cc_final: 0.8499 (mt) REVERT: B 368 ARG cc_start: 0.7985 (mmp80) cc_final: 0.7768 (mmp80) REVERT: C 189 ASN cc_start: 0.8790 (m110) cc_final: 0.8444 (m110) REVERT: C 226 THR cc_start: 0.9202 (t) cc_final: 0.8935 (t) REVERT: C 231 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7292 (p) REVERT: C 314 ILE cc_start: 0.8945 (pt) cc_final: 0.8516 (mt) REVERT: C 428 ARG cc_start: 0.6870 (mmt90) cc_final: 0.6667 (mmt90) REVERT: D 189 ASN cc_start: 0.8807 (m110) cc_final: 0.8458 (m110) REVERT: D 226 THR cc_start: 0.9189 (t) cc_final: 0.8920 (t) REVERT: D 231 CYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7296 (p) REVERT: D 314 ILE cc_start: 0.8942 (pt) cc_final: 0.8512 (mt) REVERT: D 368 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7759 (mmp80) outliers start: 27 outliers final: 15 residues processed: 205 average time/residue: 0.1068 time to fit residues: 30.7197 Evaluate side-chains 189 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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: 0.8980 chunk 129 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 222 ASN B 222 ASN C 222 ASN C 449 ASN D 200 ASN D 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124607 restraints weight = 11929.815| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.36 r_work: 0.3227 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 0.026 10848 Z= 0.150 Angle : 0.538 4.922 14764 Z= 0.290 Chirality : 0.048 0.137 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.462 16.645 1600 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.59 % Favored : 97.10 % Rotamer: Outliers : 2.67 % Allowed : 9.14 % Favored : 88.19 % 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: 0.29 (0.20), residues: 548 loop : -0.15 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 428 TYR 0.009 0.001 TYR C 253 PHE 0.017 0.002 PHE B 406 TRP 0.013 0.002 TRP B 179 HIS 0.004 0.002 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00362 (10808) covalent geometry : angle 0.53298 (14676) SS BOND : bond 0.00192 ( 32) SS BOND : angle 1.06304 ( 64) hydrogen bonds : bond 0.03166 ( 360) hydrogen bonds : angle 6.65202 ( 936) link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.16017 ( 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 202 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9192 (p) cc_final: 0.8830 (t) REVERT: A 189 ASN cc_start: 0.8884 (m110) cc_final: 0.8593 (m110) REVERT: A 314 ILE cc_start: 0.9009 (pt) cc_final: 0.8540 (mt) REVERT: A 428 ARG cc_start: 0.6972 (mmt90) cc_final: 0.6660 (mmt90) REVERT: B 89 SER cc_start: 0.9198 (p) cc_final: 0.8837 (t) REVERT: B 189 ASN cc_start: 0.8946 (m110) cc_final: 0.8659 (m110) REVERT: B 200 ASN cc_start: 0.8131 (t0) cc_final: 0.7831 (t0) REVERT: B 222 ASN cc_start: 0.7869 (t0) cc_final: 0.7429 (t0) REVERT: B 314 ILE cc_start: 0.9040 (pt) cc_final: 0.8576 (mt) REVERT: C 89 SER cc_start: 0.9195 (p) cc_final: 0.8846 (t) REVERT: C 189 ASN cc_start: 0.8935 (m110) cc_final: 0.8626 (m110) REVERT: C 200 ASN cc_start: 0.8139 (t0) cc_final: 0.7859 (t0) REVERT: C 222 ASN cc_start: 0.7824 (t0) cc_final: 0.7370 (t0) REVERT: C 314 ILE cc_start: 0.9017 (pt) cc_final: 0.8551 (mt) REVERT: C 428 ARG cc_start: 0.7184 (mmt90) cc_final: 0.6935 (mmt90) REVERT: D 89 SER cc_start: 0.9194 (p) cc_final: 0.8832 (t) REVERT: D 170 TYR cc_start: 0.8638 (m-80) cc_final: 0.8353 (m-10) REVERT: D 189 ASN cc_start: 0.8931 (m110) cc_final: 0.8616 (m-40) REVERT: D 314 ILE cc_start: 0.9053 (pt) cc_final: 0.8587 (mt) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.1046 time to fit residues: 28.4359 Evaluate side-chains 179 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 313 GLN Chi-restraints excluded: chain A residue 346 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 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 313 GLN Chi-restraints excluded: chain C residue 346 VAL 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 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: 0.8980 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117960 restraints weight = 12406.378| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.56 r_work: 0.3157 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10848 Z= 0.112 Angle : 0.492 4.419 14764 Z= 0.264 Chirality : 0.047 0.132 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.220 16.914 1600 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 11.72 % Favored : 86.47 % 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: -0.17 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.07 (0.20), residues: 548 loop : -0.15 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.006 0.001 TYR B 253 PHE 0.016 0.002 PHE D 406 TRP 0.011 0.001 TRP D 179 HIS 0.004 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00268 (10808) covalent geometry : angle 0.48811 (14676) SS BOND : bond 0.00189 ( 32) SS BOND : angle 0.89786 ( 64) hydrogen bonds : bond 0.02738 ( 360) hydrogen bonds : angle 6.27162 ( 936) link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 1.07535 ( 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 186 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9250 (p) cc_final: 0.8926 (t) REVERT: A 170 TYR cc_start: 0.8765 (m-80) cc_final: 0.8549 (m-10) REVERT: A 189 ASN cc_start: 0.9050 (m110) cc_final: 0.8714 (m-40) REVERT: A 222 ASN cc_start: 0.7966 (t0) cc_final: 0.7690 (t0) REVERT: A 311 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7578 (mm-30) REVERT: A 428 ARG cc_start: 0.7025 (mmt90) cc_final: 0.6726 (mmt90) REVERT: B 89 SER cc_start: 0.9252 (p) cc_final: 0.8932 (t) REVERT: B 170 TYR cc_start: 0.8765 (m-80) cc_final: 0.8553 (m-10) REVERT: B 189 ASN cc_start: 0.9072 (m110) cc_final: 0.8744 (m-40) REVERT: B 222 ASN cc_start: 0.7968 (t0) cc_final: 0.7658 (t0) REVERT: B 268 GLU cc_start: 0.7876 (tt0) cc_final: 0.7604 (tt0) REVERT: B 368 ARG cc_start: 0.7978 (mmp80) cc_final: 0.7642 (mmp80) REVERT: C 89 SER cc_start: 0.9249 (p) cc_final: 0.8934 (t) REVERT: C 170 TYR cc_start: 0.8757 (m-80) cc_final: 0.8546 (m-10) REVERT: C 189 ASN cc_start: 0.9042 (m110) cc_final: 0.8736 (m-40) REVERT: C 222 ASN cc_start: 0.7941 (t0) cc_final: 0.7695 (t0) REVERT: D 89 SER cc_start: 0.9233 (p) cc_final: 0.8907 (t) REVERT: D 170 TYR cc_start: 0.8769 (m-80) cc_final: 0.8560 (m-10) REVERT: D 189 ASN cc_start: 0.9054 (m110) cc_final: 0.8729 (m-40) REVERT: D 311 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7667 (mm-30) outliers start: 21 outliers final: 17 residues processed: 183 average time/residue: 0.1048 time to fit residues: 27.1895 Evaluate side-chains 159 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 287 GLU 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 231 CYS Chi-restraints excluded: chain B residue 287 GLU 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 287 GLU 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 287 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3716 r_free = 0.3716 target = 0.148891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115693 restraints weight = 12334.860| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.65 r_work: 0.3256 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10848 Z= 0.089 Angle : 0.478 5.332 14764 Z= 0.256 Chirality : 0.047 0.133 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.009 17.586 1600 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.55 % Allowed : 12.16 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.08 (0.20), residues: 552 loop : -0.13 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 428 TYR 0.007 0.001 TYR C 253 PHE 0.013 0.002 PHE C 406 TRP 0.009 0.001 TRP B 179 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00205 (10808) covalent geometry : angle 0.47493 (14676) SS BOND : bond 0.00164 ( 32) SS BOND : angle 0.82127 ( 64) hydrogen bonds : bond 0.02652 ( 360) hydrogen bonds : angle 5.98365 ( 936) link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 1.01623 ( 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 173 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.469 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: 0.9257 (p) cc_final: 0.8943 (t) REVERT: A 189 ASN cc_start: 0.9088 (m110) cc_final: 0.8767 (m-40) REVERT: A 273 ASN cc_start: 0.7337 (m-40) cc_final: 0.6969 (t0) REVERT: A 311 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7658 (mm-30) REVERT: B 89 SER cc_start: 0.9254 (p) cc_final: 0.8940 (t) REVERT: B 189 ASN cc_start: 0.9104 (m110) cc_final: 0.8784 (m-40) REVERT: B 268 GLU cc_start: 0.7845 (tt0) cc_final: 0.7528 (tt0) REVERT: B 273 ASN cc_start: 0.7291 (m-40) cc_final: 0.6941 (t0) REVERT: B 311 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7764 (mm-30) REVERT: B 368 ARG cc_start: 0.7992 (mmp80) cc_final: 0.7617 (mmp80) REVERT: C 89 SER cc_start: 0.9254 (p) cc_final: 0.8952 (t) REVERT: C 189 ASN cc_start: 0.9089 (m110) cc_final: 0.8781 (m-40) REVERT: C 311 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7775 (mm-30) REVERT: D 89 SER cc_start: 0.9253 (p) cc_final: 0.8946 (t) REVERT: D 189 ASN cc_start: 0.9083 (m110) cc_final: 0.8755 (m-40) REVERT: D 273 ASN cc_start: 0.7322 (m-40) cc_final: 0.6943 (t0) REVERT: D 311 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7696 (mm-30) outliers start: 18 outliers final: 18 residues processed: 173 average time/residue: 0.1081 time to fit residues: 26.3892 Evaluate side-chains 165 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 287 GLU 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 287 GLU 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 287 GLU Chi-restraints excluded: chain D residue 304 VAL 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: 2.9990 chunk 47 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114220 restraints weight = 12456.410| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.65 r_work: 0.3239 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10848 Z= 0.107 Angle : 0.478 5.659 14764 Z= 0.256 Chirality : 0.047 0.132 1588 Planarity : 0.004 0.043 1868 Dihedral : 3.995 16.833 1600 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 2.41 % Allowed : 12.07 % Favored : 85.52 % 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 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: 0.11 (0.20), residues: 576 loop : -0.09 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 428 TYR 0.006 0.001 TYR A 253 PHE 0.014 0.002 PHE D 406 TRP 0.008 0.001 TRP A 179 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00256 (10808) covalent geometry : angle 0.47444 (14676) SS BOND : bond 0.00188 ( 32) SS BOND : angle 0.87223 ( 64) hydrogen bonds : bond 0.02552 ( 360) hydrogen bonds : angle 5.94845 ( 936) link_NAG-ASN : bond 0.00156 ( 8) link_NAG-ASN : angle 1.08158 ( 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 181 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.351 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: 0.9205 (p) cc_final: 0.8899 (t) REVERT: A 189 ASN cc_start: 0.9094 (m110) cc_final: 0.8804 (m-40) REVERT: A 273 ASN cc_start: 0.7337 (m-40) cc_final: 0.7006 (t0) REVERT: A 311 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7628 (mm-30) REVERT: B 89 SER cc_start: 0.9267 (p) cc_final: 0.8987 (t) REVERT: B 189 ASN cc_start: 0.9106 (m110) cc_final: 0.8816 (m-40) REVERT: B 268 GLU cc_start: 0.7859 (tt0) cc_final: 0.7554 (tt0) REVERT: B 311 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7634 (mm-30) REVERT: B 368 ARG cc_start: 0.7881 (mmp80) cc_final: 0.7446 (mmp80) REVERT: C 89 SER cc_start: 0.9196 (p) cc_final: 0.8908 (t) REVERT: C 189 ASN cc_start: 0.9104 (m110) cc_final: 0.8771 (m-40) REVERT: C 273 ASN cc_start: 0.7325 (m-40) cc_final: 0.6979 (t0) REVERT: C 311 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7638 (mm-30) REVERT: D 89 SER cc_start: 0.9190 (p) cc_final: 0.8891 (t) REVERT: D 189 ASN cc_start: 0.9119 (m110) cc_final: 0.8829 (m-40) REVERT: D 273 ASN cc_start: 0.7307 (m-40) cc_final: 0.7074 (t0) outliers start: 28 outliers final: 24 residues processed: 179 average time/residue: 0.1028 time to fit residues: 26.4268 Evaluate side-chains 163 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 346 VAL 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 287 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 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 231 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 227 GLN B 275 HIS B 308 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110756 restraints weight = 12556.058| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.67 r_work: 0.3205 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10848 Z= 0.183 Angle : 0.526 5.893 14764 Z= 0.281 Chirality : 0.048 0.142 1588 Planarity : 0.004 0.046 1868 Dihedral : 4.148 16.968 1600 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.06 % Favored : 97.64 % Rotamer: Outliers : 2.59 % Allowed : 12.41 % Favored : 85.00 % 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: -0.31 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.01 (0.20), residues: 580 loop : -0.27 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 368 TYR 0.009 0.002 TYR C 276 PHE 0.020 0.002 PHE D 406 TRP 0.012 0.002 TRP B 296 HIS 0.004 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00458 (10808) covalent geometry : angle 0.52012 (14676) SS BOND : bond 0.00258 ( 32) SS BOND : angle 1.03107 ( 64) hydrogen bonds : bond 0.02725 ( 360) hydrogen bonds : angle 6.16437 ( 936) link_NAG-ASN : bond 0.00129 ( 8) link_NAG-ASN : angle 1.27509 ( 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 172 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.347 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: 0.9275 (p) cc_final: 0.9034 (t) REVERT: A 189 ASN cc_start: 0.9146 (m110) cc_final: 0.8804 (m-40) REVERT: A 311 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7737 (mm-30) REVERT: B 89 SER cc_start: 0.9274 (p) cc_final: 0.9041 (t) REVERT: B 311 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7679 (mm-30) REVERT: C 89 SER cc_start: 0.9194 (p) cc_final: 0.8941 (t) REVERT: C 189 ASN cc_start: 0.9141 (m110) cc_final: 0.8799 (m-40) REVERT: C 311 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7645 (mm-30) REVERT: D 89 SER cc_start: 0.9199 (p) cc_final: 0.8941 (t) REVERT: D 189 ASN cc_start: 0.9154 (m110) cc_final: 0.8811 (m-40) REVERT: D 311 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7736 (mm-30) outliers start: 30 outliers final: 25 residues processed: 169 average time/residue: 0.1004 time to fit residues: 24.3994 Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 362 THR 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 287 GLU Chi-restraints excluded: chain B residue 304 VAL 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 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 362 THR 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 304 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 275 HIS B 227 GLN C 227 GLN D 227 GLN D 273 ASN D 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113974 restraints weight = 12474.534| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.51 r_work: 0.3185 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10848 Z= 0.127 Angle : 0.499 6.888 14764 Z= 0.268 Chirality : 0.047 0.139 1588 Planarity : 0.004 0.045 1868 Dihedral : 4.060 17.042 1600 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.37 % Favored : 98.32 % Rotamer: Outliers : 2.41 % Allowed : 13.10 % Favored : 84.48 % 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: -0.36 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.08 (0.20), residues: 580 loop : -0.27 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.007 0.001 TYR D 276 PHE 0.019 0.002 PHE D 406 TRP 0.011 0.001 TRP D 179 HIS 0.004 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00312 (10808) covalent geometry : angle 0.49432 (14676) SS BOND : bond 0.00231 ( 32) SS BOND : angle 0.91542 ( 64) hydrogen bonds : bond 0.02550 ( 360) hydrogen bonds : angle 6.00749 ( 936) link_NAG-ASN : bond 0.00163 ( 8) link_NAG-ASN : angle 1.15559 ( 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 161 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.423 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: 0.9208 (p) cc_final: 0.8946 (t) REVERT: A 311 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7740 (mm-30) REVERT: B 89 SER cc_start: 0.9205 (p) cc_final: 0.8936 (t) REVERT: B 268 GLU cc_start: 0.7777 (tt0) cc_final: 0.7536 (tt0) REVERT: C 89 SER cc_start: 0.9195 (p) cc_final: 0.8943 (t) REVERT: C 189 ASN cc_start: 0.9126 (m110) cc_final: 0.8791 (m-40) REVERT: C 311 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7611 (mm-30) REVERT: C 428 ARG cc_start: 0.7140 (mmt90) cc_final: 0.6868 (mmt90) REVERT: D 89 SER cc_start: 0.9200 (p) cc_final: 0.8940 (t) outliers start: 28 outliers final: 25 residues processed: 159 average time/residue: 0.1036 time to fit residues: 23.7827 Evaluate side-chains 157 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 346 VAL Chi-restraints excluded: chain A residue 362 THR 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 304 VAL 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 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 362 THR 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 304 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109042 restraints weight = 12598.890| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.64 r_work: 0.3093 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10848 Z= 0.181 Angle : 0.548 8.347 14764 Z= 0.293 Chirality : 0.048 0.151 1588 Planarity : 0.004 0.047 1868 Dihedral : 4.219 16.799 1600 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.03 % Rotamer: Outliers : 2.33 % Allowed : 13.10 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.21 (0.20), residues: 580 loop : -0.51 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 428 TYR 0.011 0.002 TYR D 274 PHE 0.021 0.003 PHE A 406 TRP 0.012 0.002 TRP B 179 HIS 0.003 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00448 (10808) covalent geometry : angle 0.54280 (14676) SS BOND : bond 0.00296 ( 32) SS BOND : angle 1.04095 ( 64) hydrogen bonds : bond 0.02682 ( 360) hydrogen bonds : angle 6.22674 ( 936) link_NAG-ASN : bond 0.00112 ( 8) link_NAG-ASN : angle 1.37547 ( 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 158 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.350 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: 0.9187 (p) cc_final: 0.8947 (t) REVERT: A 311 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7671 (mm-30) REVERT: A 428 ARG cc_start: 0.7216 (mmt90) cc_final: 0.6917 (mmt90) REVERT: B 89 SER cc_start: 0.9184 (p) cc_final: 0.8952 (t) REVERT: B 128 GLU cc_start: 0.8343 (pt0) cc_final: 0.8134 (pt0) REVERT: B 268 GLU cc_start: 0.7928 (tt0) cc_final: 0.7653 (tt0) REVERT: C 89 SER cc_start: 0.9176 (p) cc_final: 0.8947 (t) REVERT: C 428 ARG cc_start: 0.7072 (mmt90) cc_final: 0.6824 (mmt90) REVERT: D 89 SER cc_start: 0.9189 (p) cc_final: 0.8956 (t) outliers start: 27 outliers final: 27 residues processed: 155 average time/residue: 0.1045 time to fit residues: 23.1889 Evaluate side-chains 150 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR 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 304 VAL 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 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 362 THR 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 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3669 r_free = 0.3669 target = 0.145001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112292 restraints weight = 12456.993| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.58 r_work: 0.3234 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10848 Z= 0.115 Angle : 0.502 8.021 14764 Z= 0.271 Chirality : 0.047 0.140 1588 Planarity : 0.004 0.044 1868 Dihedral : 4.064 17.109 1600 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.45 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 13.19 % Favored : 84.48 % 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: -0.57 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.25 (0.19), residues: 580 loop : -0.38 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 428 TYR 0.010 0.001 TYR C 274 PHE 0.018 0.002 PHE A 406 TRP 0.011 0.001 TRP D 179 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00280 (10808) covalent geometry : angle 0.49806 (14676) SS BOND : bond 0.00228 ( 32) SS BOND : angle 0.87976 ( 64) hydrogen bonds : bond 0.02490 ( 360) hydrogen bonds : angle 5.98452 ( 936) link_NAG-ASN : bond 0.00157 ( 8) link_NAG-ASN : angle 1.19160 ( 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 166 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9200 (p) cc_final: 0.8947 (t) REVERT: A 311 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7731 (mm-30) REVERT: A 428 ARG cc_start: 0.7214 (mmt90) cc_final: 0.6975 (mmt90) REVERT: B 89 SER cc_start: 0.9206 (p) cc_final: 0.8952 (t) REVERT: B 128 GLU cc_start: 0.8320 (pt0) cc_final: 0.8097 (pt0) REVERT: B 268 GLU cc_start: 0.7845 (tt0) cc_final: 0.7593 (tt0) REVERT: C 89 SER cc_start: 0.9192 (p) cc_final: 0.8947 (t) REVERT: C 189 ASN cc_start: 0.9165 (m110) cc_final: 0.8824 (m-40) REVERT: D 89 SER cc_start: 0.9199 (p) cc_final: 0.8951 (t) outliers start: 27 outliers final: 27 residues processed: 163 average time/residue: 0.1065 time to fit residues: 24.8607 Evaluate side-chains 152 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 362 THR 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 304 VAL 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 287 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 362 THR 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 304 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.0060 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 GLN C 227 GLN D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112359 restraints weight = 12576.418| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.60 r_work: 0.3248 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10848 Z= 0.136 Angle : 0.581 14.350 14764 Z= 0.306 Chirality : 0.050 0.327 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.099 16.915 1600 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 2.59 % Allowed : 13.19 % Favored : 84.22 % 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: -0.57 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.28 (0.20), residues: 580 loop : -0.36 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 428 TYR 0.011 0.001 TYR A 274 PHE 0.019 0.002 PHE B 406 TRP 0.010 0.001 TRP D 179 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00352 (10808) covalent geometry : angle 0.56284 (14676) SS BOND : bond 0.00639 ( 32) SS BOND : angle 2.15663 ( 64) hydrogen bonds : bond 0.02548 ( 360) hydrogen bonds : angle 6.02606 ( 936) link_NAG-ASN : bond 0.00129 ( 8) link_NAG-ASN : angle 1.16729 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.09 seconds wall clock time: 42 minutes 49.14 seconds (2569.14 seconds total)