Starting phenix.real_space_refine on Mon Jul 28 18:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2q_26318/07_2025/7u2q_26318.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2q_26318/07_2025/7u2q_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_26318/07_2025/7u2q_26318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2q_26318/07_2025/7u2q_26318.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2q_26318/07_2025/7u2q_26318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2q_26318/07_2025/7u2q_26318.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ASN:plan1': 1, 'ASP:plan': 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: C, B, D Time building chain proxies: 5.48, per 1000 atoms: 0.52 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 C 92 " - pdb=" SG CYS C 417 " distance=2.02 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.02 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.02 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.07 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 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: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.61 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: 3.61 Time building geometry restraints manager: 3.21 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.590 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.740 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (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 TRP 0.019 0.003 TRP D 179 HIS 0.003 0.001 HIS D 275 PHE 0.019 0.004 PHE B 406 TYR 0.038 0.007 TYR D 276 ARG 0.003 0.001 ARG C 225 Details of bonding type rmsd link_NAG-ASN : bond 0.04454 ( 8) link_NAG-ASN : angle 1.92144 ( 24) hydrogen bonds : bond 0.17420 ( 360) hydrogen bonds : angle 9.02785 ( 936) SS BOND : bond 0.01370 ( 32) SS BOND : angle 3.57937 ( 64) covalent geometry : bond 0.01349 (10808) covalent geometry : angle 1.51862 (14676) *********************** 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 : 1.331 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: 0.2424 time to fit residues: 116.7632 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN B 189 ASN B 369 ASN C 369 ASN D 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122244 restraints weight = 11896.925| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.39 r_work: 0.3312 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2511 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= 0.135 Angle : 0.585 5.098 14764 Z= 0.320 Chirality : 0.048 0.132 1588 Planarity : 0.005 0.036 1868 Dihedral : 4.849 16.061 1600 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 2.33 % Allowed : 8.62 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.24 (0.21), residues: 516 loop : -0.09 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 179 HIS 0.004 0.001 HIS C 185 PHE 0.022 0.002 PHE D 406 TYR 0.011 0.001 TYR A 253 ARG 0.006 0.001 ARG D 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 1.28559 ( 24) hydrogen bonds : bond 0.03787 ( 360) hydrogen bonds : angle 6.95075 ( 936) SS BOND : bond 0.00238 ( 32) SS BOND : angle 1.18772 ( 64) covalent geometry : bond 0.00307 (10808) covalent geometry : angle 0.57926 (14676) *********************** 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 206 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.368 Fit side-chains REVERT: A 200 ASN cc_start: 0.8002 (t0) cc_final: 0.7799 (t0) REVERT: A 226 THR cc_start: 0.9221 (t) cc_final: 0.8957 (t) REVERT: A 231 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7356 (p) REVERT: A 268 GLU cc_start: 0.7746 (tt0) cc_final: 0.7453 (tt0) REVERT: A 314 ILE cc_start: 0.8995 (pt) cc_final: 0.8544 (mt) REVERT: B 189 ASN cc_start: 0.8856 (m110) cc_final: 0.8511 (m110) REVERT: B 226 THR cc_start: 0.9214 (t) cc_final: 0.8952 (t) REVERT: B 231 CYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 268 GLU cc_start: 0.7735 (tt0) cc_final: 0.7439 (tt0) REVERT: B 314 ILE cc_start: 0.8994 (pt) cc_final: 0.8549 (mt) REVERT: B 368 ARG cc_start: 0.8018 (mmp80) cc_final: 0.7806 (mmp80) REVERT: B 428 ARG cc_start: 0.6881 (mmt90) cc_final: 0.6647 (mmt90) REVERT: C 189 ASN cc_start: 0.8899 (m-40) cc_final: 0.8592 (m110) REVERT: C 226 THR cc_start: 0.9228 (t) cc_final: 0.8964 (t) REVERT: C 231 CYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7342 (p) REVERT: C 314 ILE cc_start: 0.9002 (pt) cc_final: 0.8562 (mt) REVERT: C 428 ARG cc_start: 0.6863 (mmt90) cc_final: 0.6622 (mmt90) REVERT: D 226 THR cc_start: 0.9217 (t) cc_final: 0.8949 (t) REVERT: D 231 CYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7346 (p) REVERT: D 268 GLU cc_start: 0.7757 (tt0) cc_final: 0.7473 (tt0) REVERT: D 314 ILE cc_start: 0.8998 (pt) cc_final: 0.8558 (mt) REVERT: D 428 ARG cc_start: 0.6846 (mmt90) cc_final: 0.6609 (mmt90) outliers start: 27 outliers final: 15 residues processed: 199 average time/residue: 0.2838 time to fit residues: 81.3638 Evaluate side-chains 181 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.149642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120028 restraints weight = 12130.277| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.38 r_work: 0.3193 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10848 Z= 0.182 Angle : 0.556 4.818 14764 Z= 0.300 Chirality : 0.049 0.142 1588 Planarity : 0.005 0.042 1868 Dihedral : 4.540 16.573 1600 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.44 % Favored : 97.26 % Rotamer: Outliers : 1.98 % Allowed : 10.09 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.25 (0.20), residues: 548 loop : -0.26 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 179 HIS 0.004 0.002 HIS C 185 PHE 0.021 0.003 PHE D 406 TYR 0.007 0.001 TYR C 253 ARG 0.006 0.001 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 8) link_NAG-ASN : angle 1.21101 ( 24) hydrogen bonds : bond 0.03271 ( 360) hydrogen bonds : angle 6.76187 ( 936) SS BOND : bond 0.00222 ( 32) SS BOND : angle 1.12556 ( 64) covalent geometry : bond 0.00450 (10808) covalent geometry : angle 0.55040 (14676) *********************** 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 191 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9203 (p) cc_final: 0.8882 (t) REVERT: A 170 TYR cc_start: 0.8657 (m-80) cc_final: 0.8424 (m-10) REVERT: A 200 ASN cc_start: 0.8164 (t0) cc_final: 0.7948 (t0) REVERT: A 268 GLU cc_start: 0.7958 (tt0) cc_final: 0.7721 (tt0) REVERT: A 314 ILE cc_start: 0.9018 (pt) cc_final: 0.8514 (mt) REVERT: B 89 SER cc_start: 0.9208 (p) cc_final: 0.8891 (t) REVERT: B 170 TYR cc_start: 0.8656 (m-80) cc_final: 0.8421 (m-10) REVERT: B 189 ASN cc_start: 0.8983 (m110) cc_final: 0.8699 (m110) REVERT: B 200 ASN cc_start: 0.8144 (t0) cc_final: 0.7821 (t0) REVERT: B 268 GLU cc_start: 0.7937 (tt0) cc_final: 0.7702 (tt0) REVERT: B 314 ILE cc_start: 0.9013 (pt) cc_final: 0.8507 (mt) REVERT: C 89 SER cc_start: 0.9119 (p) cc_final: 0.8789 (t) REVERT: C 170 TYR cc_start: 0.8656 (m-80) cc_final: 0.8423 (m-10) REVERT: C 200 ASN cc_start: 0.8211 (t0) cc_final: 0.7963 (t0) REVERT: C 314 ILE cc_start: 0.9022 (pt) cc_final: 0.8518 (mt) REVERT: D 89 SER cc_start: 0.9114 (p) cc_final: 0.8777 (t) REVERT: D 170 TYR cc_start: 0.8664 (m-80) cc_final: 0.8439 (m-10) REVERT: D 200 ASN cc_start: 0.8142 (t0) cc_final: 0.7865 (t0) REVERT: D 314 ILE cc_start: 0.9018 (pt) cc_final: 0.8521 (mt) outliers start: 23 outliers final: 20 residues processed: 184 average time/residue: 0.3921 time to fit residues: 99.1029 Evaluate side-chains 172 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 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 B residue 396 ILE 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 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 40 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114887 restraints weight = 12423.463| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.59 r_work: 0.3156 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3283 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= 0.120 Angle : 0.492 4.551 14764 Z= 0.264 Chirality : 0.047 0.130 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.228 17.062 1600 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.72 % Allowed : 12.24 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.20 (0.20), residues: 568 loop : -0.25 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 179 HIS 0.005 0.001 HIS B 185 PHE 0.016 0.002 PHE A 406 TYR 0.007 0.001 TYR D 253 ARG 0.006 0.000 ARG C 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 1.07064 ( 24) hydrogen bonds : bond 0.02724 ( 360) hydrogen bonds : angle 6.26260 ( 936) SS BOND : bond 0.00184 ( 32) SS BOND : angle 0.92416 ( 64) covalent geometry : bond 0.00289 (10808) covalent geometry : angle 0.48821 (14676) *********************** 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 173 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9186 (p) cc_final: 0.8876 (t) REVERT: A 227 GLN cc_start: 0.8978 (mt0) cc_final: 0.8728 (mt0) REVERT: A 268 GLU cc_start: 0.7841 (tt0) cc_final: 0.7479 (tt0) REVERT: A 311 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7676 (mm-30) REVERT: B 89 SER cc_start: 0.9185 (p) cc_final: 0.8871 (t) REVERT: B 189 ASN cc_start: 0.9066 (m110) cc_final: 0.8759 (m110) REVERT: B 227 GLN cc_start: 0.8982 (mt0) cc_final: 0.8736 (mt0) REVERT: C 89 SER cc_start: 0.9182 (p) cc_final: 0.8885 (t) REVERT: C 311 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7770 (mm-30) REVERT: D 89 SER cc_start: 0.9180 (p) cc_final: 0.8871 (t) REVERT: D 227 GLN cc_start: 0.8978 (mt0) cc_final: 0.8727 (mt0) outliers start: 20 outliers final: 17 residues processed: 170 average time/residue: 0.3072 time to fit residues: 74.6839 Evaluate side-chains 148 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 313 GLN Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 287 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 0.0070 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.145831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112779 restraints weight = 12375.220| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.61 r_work: 0.3253 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3440 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= 0.135 Angle : 0.503 5.560 14764 Z= 0.268 Chirality : 0.047 0.131 1588 Planarity : 0.004 0.044 1868 Dihedral : 4.173 17.366 1600 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 2.41 % Allowed : 11.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.07 (0.20), residues: 576 loop : -0.29 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 179 HIS 0.005 0.001 HIS C 185 PHE 0.017 0.002 PHE B 406 TYR 0.009 0.001 TYR D 274 ARG 0.004 0.000 ARG C 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 8) link_NAG-ASN : angle 1.15854 ( 24) hydrogen bonds : bond 0.02752 ( 360) hydrogen bonds : angle 6.22824 ( 936) SS BOND : bond 0.00212 ( 32) SS BOND : angle 0.91722 ( 64) covalent geometry : bond 0.00330 (10808) covalent geometry : angle 0.49863 (14676) *********************** 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 162 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 2.208 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: 0.9194 (p) cc_final: 0.8912 (t) REVERT: A 311 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7698 (mm-30) REVERT: B 89 SER cc_start: 0.9193 (p) cc_final: 0.8910 (t) REVERT: B 189 ASN cc_start: 0.9138 (m110) cc_final: 0.8807 (m-40) REVERT: C 89 SER cc_start: 0.9192 (p) cc_final: 0.8927 (t) REVERT: C 311 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7781 (mm-30) REVERT: D 89 SER cc_start: 0.9195 (p) cc_final: 0.8916 (t) REVERT: D 428 ARG cc_start: 0.7109 (mmt90) cc_final: 0.6831 (mmt90) outliers start: 28 outliers final: 26 residues processed: 158 average time/residue: 0.3508 time to fit residues: 79.2727 Evaluate side-chains 153 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 B residue 396 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 304 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 Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 0.0060 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- 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 D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118744 restraints weight = 12226.538| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.54 r_work: 0.3276 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10848 Z= 0.084 Angle : 0.466 5.796 14764 Z= 0.250 Chirality : 0.047 0.130 1588 Planarity : 0.004 0.042 1868 Dihedral : 3.962 17.672 1600 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % Rotamer: Outliers : 1.38 % Allowed : 14.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1312 helix: None (None), residues: 0 sheet: 0.07 (0.20), residues: 576 loop : -0.12 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 179 HIS 0.002 0.001 HIS A 185 PHE 0.012 0.002 PHE D 406 TYR 0.006 0.001 TYR A 253 ARG 0.003 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 0.99238 ( 24) hydrogen bonds : bond 0.02585 ( 360) hydrogen bonds : angle 5.83858 ( 936) SS BOND : bond 0.00169 ( 32) SS BOND : angle 0.80536 ( 64) covalent geometry : bond 0.00193 (10808) covalent geometry : angle 0.46279 (14676) *********************** 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 156 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9197 (p) cc_final: 0.8907 (t) REVERT: A 311 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7708 (mm-30) REVERT: A 428 ARG cc_start: 0.7122 (mmt90) cc_final: 0.6818 (mmt90) REVERT: B 89 SER cc_start: 0.9191 (p) cc_final: 0.8903 (t) REVERT: B 189 ASN cc_start: 0.9113 (m110) cc_final: 0.8846 (m-40) REVERT: B 428 ARG cc_start: 0.7081 (mmt90) cc_final: 0.6750 (mmt90) REVERT: C 89 SER cc_start: 0.9195 (p) cc_final: 0.8917 (t) REVERT: C 311 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7684 (mm-30) REVERT: C 428 ARG cc_start: 0.7106 (mmt90) cc_final: 0.6854 (mmt90) REVERT: D 89 SER cc_start: 0.9196 (p) cc_final: 0.8908 (t) outliers start: 16 outliers final: 16 residues processed: 156 average time/residue: 0.2126 time to fit residues: 47.9925 Evaluate side-chains 147 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 304 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS B 275 HIS C 227 GLN C 275 HIS C 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114893 restraints weight = 12518.405| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.63 r_work: 0.3265 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10848 Z= 0.123 Angle : 0.541 11.052 14764 Z= 0.286 Chirality : 0.049 0.310 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.016 17.417 1600 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.03 (0.20), residues: 576 loop : -0.15 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 179 HIS 0.003 0.001 HIS B 185 PHE 0.014 0.002 PHE D 406 TYR 0.008 0.001 TYR C 274 ARG 0.003 0.000 ARG D 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 8) link_NAG-ASN : angle 1.08204 ( 24) hydrogen bonds : bond 0.02642 ( 360) hydrogen bonds : angle 5.92096 ( 936) SS BOND : bond 0.00685 ( 32) SS BOND : angle 2.00703 ( 64) covalent geometry : bond 0.00307 (10808) covalent geometry : angle 0.52462 (14676) *********************** 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 161 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9202 (p) cc_final: 0.8931 (t) REVERT: A 311 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7692 (mm-30) REVERT: B 89 SER cc_start: 0.9193 (p) cc_final: 0.8919 (t) REVERT: C 89 SER cc_start: 0.9191 (p) cc_final: 0.8931 (t) REVERT: C 311 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7719 (mm-30) REVERT: D 89 SER cc_start: 0.9201 (p) cc_final: 0.8927 (t) REVERT: D 186 ASP cc_start: 0.7936 (p0) cc_final: 0.7728 (p0) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.2238 time to fit residues: 50.7822 Evaluate side-chains 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 362 THR 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 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN D 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.117124 restraints weight = 12301.015| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.55 r_work: 0.3244 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10848 Z= 0.116 Angle : 0.562 16.294 14764 Z= 0.295 Chirality : 0.048 0.246 1588 Planarity : 0.004 0.043 1868 Dihedral : 4.023 17.073 1600 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.37 % Favored : 98.32 % Rotamer: Outliers : 2.24 % Allowed : 12.84 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: 0.01 (0.20), residues: 580 loop : -0.17 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 179 HIS 0.003 0.001 HIS A 185 PHE 0.017 0.002 PHE B 406 TYR 0.009 0.001 TYR C 274 ARG 0.004 0.000 ARG B 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 8) link_NAG-ASN : angle 1.04177 ( 24) hydrogen bonds : bond 0.02608 ( 360) hydrogen bonds : angle 5.96856 ( 936) SS BOND : bond 0.00713 ( 32) SS BOND : angle 1.78623 ( 64) covalent geometry : bond 0.00287 (10808) covalent geometry : angle 0.54939 (14676) *********************** 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: 26 poor density : 135 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9201 (p) cc_final: 0.8939 (t) REVERT: A 311 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7743 (mm-30) REVERT: B 89 SER cc_start: 0.9199 (p) cc_final: 0.8934 (t) REVERT: C 89 SER cc_start: 0.9197 (p) cc_final: 0.8951 (t) REVERT: D 89 SER cc_start: 0.9205 (p) cc_final: 0.8942 (t) REVERT: D 186 ASP cc_start: 0.7933 (p0) cc_final: 0.7712 (p0) outliers start: 26 outliers final: 22 residues processed: 161 average time/residue: 0.2462 time to fit residues: 56.9975 Evaluate side-chains 149 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 304 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 362 THR 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 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 449 ASN D 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113445 restraints weight = 12621.521| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.62 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10848 Z= 0.148 Angle : 0.605 15.895 14764 Z= 0.316 Chirality : 0.050 0.278 1588 Planarity : 0.004 0.044 1868 Dihedral : 4.103 17.445 1600 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 2.16 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.04 (0.20), residues: 576 loop : -0.30 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.002 0.001 HIS C 185 PHE 0.019 0.002 PHE A 406 TYR 0.008 0.001 TYR B 274 ARG 0.004 0.000 ARG D 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 8) link_NAG-ASN : angle 1.11576 ( 24) hydrogen bonds : bond 0.02656 ( 360) hydrogen bonds : angle 6.08227 ( 936) SS BOND : bond 0.00828 ( 32) SS BOND : angle 2.14730 ( 64) covalent geometry : bond 0.00378 (10808) covalent geometry : angle 0.58789 (14676) *********************** 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 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9185 (p) cc_final: 0.8920 (t) REVERT: A 311 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7727 (mm-30) REVERT: B 89 SER cc_start: 0.9178 (p) cc_final: 0.8918 (t) REVERT: C 89 SER cc_start: 0.9177 (p) cc_final: 0.8928 (t) REVERT: C 428 ARG cc_start: 0.7116 (mmt90) cc_final: 0.6814 (mmt90) REVERT: D 89 SER cc_start: 0.9183 (p) cc_final: 0.8925 (t) REVERT: D 186 ASP cc_start: 0.7932 (p0) cc_final: 0.7697 (p0) outliers start: 25 outliers final: 24 residues processed: 151 average time/residue: 0.2270 time to fit residues: 48.4822 Evaluate side-chains 150 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 B residue 362 THR 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 362 THR 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 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117579 restraints weight = 12366.305| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.53 r_work: 0.3180 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10848 Z= 0.122 Angle : 0.584 15.932 14764 Z= 0.306 Chirality : 0.049 0.227 1588 Planarity : 0.004 0.042 1868 Dihedral : 4.052 17.207 1600 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 2.07 % Allowed : 13.28 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.09 (0.20), residues: 576 loop : -0.21 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.002 0.001 HIS C 185 PHE 0.017 0.002 PHE A 406 TYR 0.009 0.001 TYR A 274 ARG 0.004 0.000 ARG D 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 1.00291 ( 24) hydrogen bonds : bond 0.02642 ( 360) hydrogen bonds : angle 5.98736 ( 936) SS BOND : bond 0.00810 ( 32) SS BOND : angle 1.93770 ( 64) covalent geometry : bond 0.00309 (10808) covalent geometry : angle 0.57034 (14676) ********************** 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 158 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 SER cc_start: 0.9166 (p) cc_final: 0.8913 (t) REVERT: A 311 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7727 (mm-30) REVERT: B 89 SER cc_start: 0.9160 (p) cc_final: 0.8912 (t) REVERT: C 89 SER cc_start: 0.9161 (p) cc_final: 0.8917 (t) REVERT: C 428 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6885 (mmt90) REVERT: D 89 SER cc_start: 0.9173 (p) cc_final: 0.8915 (t) outliers start: 24 outliers final: 21 residues processed: 158 average time/residue: 0.2281 time to fit residues: 50.8083 Evaluate side-chains 147 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 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 304 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 102 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 D 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113550 restraints weight = 12480.225| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.59 r_work: 0.3215 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10848 Z= 0.152 Angle : 0.609 16.023 14764 Z= 0.319 Chirality : 0.050 0.232 1588 Planarity : 0.004 0.044 1868 Dihedral : 4.145 17.884 1600 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 1.52 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 13.28 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1312 helix: None (None), residues: 0 sheet: -0.13 (0.20), residues: 576 loop : -0.31 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 179 HIS 0.003 0.001 HIS A 185 PHE 0.019 0.002 PHE A 406 TYR 0.010 0.001 TYR B 274 ARG 0.004 0.000 ARG D 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 8) link_NAG-ASN : angle 1.11198 ( 24) hydrogen bonds : bond 0.02673 ( 360) hydrogen bonds : angle 6.11732 ( 936) SS BOND : bond 0.00834 ( 32) SS BOND : angle 2.02268 ( 64) covalent geometry : bond 0.00388 (10808) covalent geometry : angle 0.59461 (14676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.50 seconds wall clock time: 101 minutes 19.46 seconds (6079.46 seconds total)