Starting phenix.real_space_refine on Thu Jul 2 10:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.map" model { file = "/net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pja_71685/07_2026/9pja_71685.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 46 5.16 5 C 5146 2.51 5 N 1383 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8077 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3940 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3930 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 485, 3930 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 4013 Chain: "A" Number of atoms: 3937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3927 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 485, 3927 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 464} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 4010 Chain: "C" 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 Chain: "D" 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 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'ACO': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'ACO': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS B 416 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 416 " occ=0.50 residue: pdb=" N AHIS A 416 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 416 " occ=0.50 Time building chain proxies: 2.70, per 1000 atoms: 0.33 Number of scatterers: 8077 At special positions: 0 Unit cell: (73.983, 135.771, 80.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 6 15.00 O 1496 8.00 N 1383 7.00 C 5146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS B 252 " distance=2.02 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 330 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 231 " - pdb=" SG CYS A 252 " distance=2.02 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 330 " distance=2.04 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 547 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 602 " - " ASN A 93 " " NAG B 602 " - " ASN B 93 " " NAG B 603 " - " ASN B 211 " " NAG C 1 " - " ASN B 161 " " NAG D 1 " - " ASN A 161 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 32.2% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 91 through 94 Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.671A pdb=" N ASN B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.770A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.801A pdb=" N HIS B 441 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 443 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 468 removed outlier: 4.128A pdb=" N PHE B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 491 through 506 removed outlier: 3.638A pdb=" N GLY B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 524 Processing helix chain 'B' and resid 531 through 547 Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 91 through 94 Processing helix chain 'A' and resid 185 through 197 removed outlier: 3.669A pdb=" N ASN A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.719A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 390 through 393 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.856A pdb=" N HIS A 441 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 443 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 468 removed outlier: 4.134A pdb=" N PHE A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 491 Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.504A pdb=" N GLY A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 531 through 547 Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 106 removed outlier: 5.408A pdb=" N HIS B 100 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 125 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP B 119 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 163 " --> pdb=" O PHE B 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 113 removed outlier: 5.697A pdb=" N TYR B 112 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 283 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 5.697A pdb=" N TYR B 112 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 138 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER B 153 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY B 318 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 230 through 235 removed outlier: 5.221A pdb=" N GLU B 219 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE B 205 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 210 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU B 255 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 372 through 373 removed outlier: 6.247A pdb=" N THR B 432 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE B 474 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE B 434 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS B 476 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 436 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 106 removed outlier: 4.483A pdb=" N ARG A 125 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR A 99 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 123 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N SER A 101 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 11.065A pdb=" N LEU A 121 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N ALA A 103 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N ASP A 119 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N ILE A 105 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 12.374A pdb=" N GLN A 117 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.689A pdb=" N PHE A 138 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.689A pdb=" N PHE A 138 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 230 through 235 removed outlier: 5.238A pdb=" N GLU A 219 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 210 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU A 255 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AB2, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.307A pdb=" N THR A 432 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 474 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 434 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS A 476 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 436 " --> pdb=" O LYS A 476 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 981 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: 1.34 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1421 1.32 - 1.45: 2193 1.45 - 1.57: 4579 1.57 - 1.69: 10 1.69 - 1.82: 72 Bond restraints: 8275 Sorted by residual: bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 8270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10803 1.36 - 2.72: 339 2.72 - 4.08: 62 4.08 - 5.45: 11 5.45 - 6.81: 5 Bond angle restraints: 11220 Sorted by residual: angle pdb=" CA MET A 285 " pdb=" CB MET A 285 " pdb=" CG MET A 285 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CB MET A 285 " pdb=" CG MET A 285 " pdb=" SD MET A 285 " ideal model delta sigma weight residual 112.70 106.05 6.65 3.00e+00 1.11e-01 4.92e+00 angle pdb=" C BHIS A 416 " pdb=" CA BHIS A 416 " pdb=" CB BHIS A 416 " ideal model delta sigma weight residual 109.48 113.13 -3.65 1.68e+00 3.54e-01 4.72e+00 angle pdb=" C7P ACO B 601 " pdb=" N8P ACO B 601 " pdb=" C9P ACO B 601 " ideal model delta sigma weight residual 122.54 125.25 -2.71 1.28e+00 6.06e-01 4.44e+00 angle pdb=" C MET A 285 " pdb=" CA MET A 285 " pdb=" CB MET A 285 " ideal model delta sigma weight residual 109.75 113.27 -3.52 1.72e+00 3.38e-01 4.20e+00 ... (remaining 11215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4530 17.66 - 35.33: 433 35.33 - 52.99: 87 52.99 - 70.65: 35 70.65 - 88.32: 11 Dihedral angle restraints: 5096 sinusoidal: 2262 harmonic: 2834 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 547 " pdb=" CB CYS A 547 " ideal model delta sinusoidal sigma weight residual -86.00 -146.35 60.35 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 547 " pdb=" CB CYS B 547 " ideal model delta sinusoidal sigma weight residual -86.00 -141.78 55.78 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA ARG B 392 " pdb=" C ARG B 392 " pdb=" N HIS B 393 " pdb=" CA HIS B 393 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 980 0.048 - 0.095: 209 0.095 - 0.143: 58 0.143 - 0.190: 2 0.190 - 0.238: 2 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CAP ACO B 601 " pdb=" C9P ACO B 601 " pdb=" CBP ACO B 601 " pdb=" OAP ACO B 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.07 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CAP ACO A 601 " pdb=" C9P ACO A 601 " pdb=" CBP ACO A 601 " pdb=" OAP ACO A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.08 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1248 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 64 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 65 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 64 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 65 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB BHIS A 416 " -0.009 2.00e-02 2.50e+03 1.16e-02 2.01e+00 pdb=" CG BHIS A 416 " 0.024 2.00e-02 2.50e+03 pdb=" ND1BHIS A 416 " -0.004 2.00e-02 2.50e+03 pdb=" CD2BHIS A 416 " -0.010 2.00e-02 2.50e+03 pdb=" CE1BHIS A 416 " -0.004 2.00e-02 2.50e+03 pdb=" NE2BHIS A 416 " 0.003 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 414 2.73 - 3.27: 7863 3.27 - 3.81: 13970 3.81 - 4.36: 17594 4.36 - 4.90: 30379 Nonbonded interactions: 70220 Sorted by model distance: nonbonded pdb=" OE1 GLU A 422 " pdb=" NH2 ARG A 425 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 523 " pdb=" OD1 ASN A 537 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR B 523 " pdb=" OD1 ASN B 537 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 134 " pdb=" OE2 GLU B 187 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 260 " pdb=" O THR B 407 " model vdw 2.228 3.040 ... (remaining 70215 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 63 through 64 and (name N or name CA or name C or name O \ or name CB )) or resid 65 through 304 or (resid 305 and (name N or name CA or na \ me C or name O or name CB )) or resid 306 through 415 or resid 417 through 602)) \ selection = (chain 'B' and (resid 63 through 297 or (resid 298 through 302 and (name N or na \ me CA or name C or name O or name CB )) or resid 303 through 415 or resid 417 th \ rough 602)) } ncs_group { reference = 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=0.50 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: 6.640 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.003 0.035 8292 Z= 0.154 Angle : 0.587 6.807 11261 Z= 0.302 Chirality : 0.043 0.238 1251 Planarity : 0.004 0.041 1411 Dihedral : 15.030 88.317 3242 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 0.00 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.07 (0.27), residues: 972 helix: 1.62 (0.32), residues: 268 sheet: -0.56 (0.31), residues: 250 loop : -0.47 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 261 TYR 0.013 0.001 TYR B 499 PHE 0.015 0.001 PHE B 506 TRP 0.008 0.001 TRP B 398 HIS 0.004 0.000 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8275) covalent geometry : angle 0.58172 / 0.30 (11220) SS BOND : bond 0.00344 / 0.22 ( 10) SS BOND : angle 1.22543 / 0.86 ( 20) hydrogen bonds : bond 0.11176 / 7.91 ( 343) hydrogen bonds : angle 7.01760 / 4.72 ( 981) link_BETA1-4 : bond 0.00531 / 0.27 ( 2) link_BETA1-4 : angle 1.30320 / 0.66 ( 6) link_NAG-ASN : bond 0.00288 / 0.14 ( 5) link_NAG-ASN : angle 1.75371 / 1.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8406 (t80) cc_final: 0.8127 (t80) REVERT: A 448 ASP cc_start: 0.7464 (m-30) cc_final: 0.7235 (m-30) REVERT: A 483 MET cc_start: 0.8405 (tpp) cc_final: 0.8169 (tpp) REVERT: A 528 ILE cc_start: 0.7927 (tp) cc_final: 0.7611 (tt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5059 time to fit residues: 71.0380 Evaluate side-chains 100 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 HIS B 397 GLN B 529 HIS A 130 GLN ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110067 restraints weight = 24749.671| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.12 r_work: 0.3133 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8292 Z= 0.302 Angle : 0.691 8.699 11261 Z= 0.357 Chirality : 0.049 0.256 1251 Planarity : 0.005 0.041 1411 Dihedral : 10.725 61.737 1315 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 8.92 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.16 (0.26), residues: 972 helix: 1.27 (0.31), residues: 266 sheet: -0.71 (0.31), residues: 246 loop : -0.48 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.019 0.002 TYR A 112 PHE 0.013 0.002 PHE A 445 TRP 0.011 0.002 TRP B 398 HIS 0.007 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.30 ( 8275) covalent geometry : angle 0.68352 / 0.35 (11220) SS BOND : bond 0.00676 / 0.39 ( 10) SS BOND : angle 1.73555 / 1.28 ( 20) hydrogen bonds : bond 0.04443 / 3.12 ( 343) hydrogen bonds : angle 5.93316 / 4.02 ( 981) link_BETA1-4 : bond 0.00330 / 0.17 ( 2) link_BETA1-4 : angle 1.41794 / 0.70 ( 6) link_NAG-ASN : bond 0.00441 / 0.26 ( 5) link_NAG-ASN : angle 2.00834 / 1.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8519 (t80) cc_final: 0.8176 (t80) REVERT: B 388 LEU cc_start: 0.7977 (tt) cc_final: 0.7673 (tt) REVERT: B 528 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7158 (tp) REVERT: A 448 ASP cc_start: 0.8106 (m-30) cc_final: 0.7770 (m-30) REVERT: A 483 MET cc_start: 0.8212 (tpp) cc_final: 0.8001 (tpp) outliers start: 13 outliers final: 8 residues processed: 113 average time/residue: 0.5021 time to fit residues: 60.1104 Evaluate side-chains 102 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 529 HIS ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.114175 restraints weight = 23702.683| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.07 r_work: 0.3174 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8292 Z= 0.152 Angle : 0.561 7.834 11261 Z= 0.293 Chirality : 0.044 0.248 1251 Planarity : 0.004 0.040 1411 Dihedral : 10.374 58.172 1315 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.74 % Allowed : 11.24 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.00 (0.27), residues: 972 helix: 1.56 (0.32), residues: 266 sheet: -0.78 (0.31), residues: 246 loop : -0.38 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 72 TYR 0.014 0.001 TYR B 499 PHE 0.011 0.001 PHE A 445 TRP 0.014 0.001 TRP A 398 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8275) covalent geometry : angle 0.55526 / 0.29 (11220) SS BOND : bond 0.00367 / 0.22 ( 10) SS BOND : angle 1.03536 / 0.76 ( 20) hydrogen bonds : bond 0.03500 / 2.47 ( 343) hydrogen bonds : angle 5.52733 / 3.76 ( 981) link_BETA1-4 : bond 0.00410 / 0.21 ( 2) link_BETA1-4 : angle 1.10403 / 0.53 ( 6) link_NAG-ASN : bond 0.00290 / 0.15 ( 5) link_NAG-ASN : angle 1.90218 / 1.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 131 ARG cc_start: 0.7886 (ttt-90) cc_final: 0.7653 (ttp80) REVERT: B 173 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: B 339 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7034 (tptt) REVERT: B 363 TYR cc_start: 0.8497 (t80) cc_final: 0.8109 (t80) REVERT: B 528 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7324 (tt) REVERT: A 126 ASP cc_start: 0.7745 (p0) cc_final: 0.7295 (p0) REVERT: A 391 GLU cc_start: 0.6753 (pm20) cc_final: 0.6495 (pm20) REVERT: A 448 ASP cc_start: 0.7923 (m-30) cc_final: 0.7569 (m-30) REVERT: A 483 MET cc_start: 0.8160 (tpp) cc_final: 0.7938 (tpp) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 0.4472 time to fit residues: 53.7721 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 529 HIS A 130 GLN ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112562 restraints weight = 25584.134| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.39 r_work: 0.3147 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8292 Z= 0.166 Angle : 0.565 7.554 11261 Z= 0.297 Chirality : 0.044 0.248 1251 Planarity : 0.004 0.039 1411 Dihedral : 10.187 58.435 1315 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.85 % Allowed : 12.63 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.05 (0.27), residues: 972 helix: 1.63 (0.32), residues: 266 sheet: -0.78 (0.31), residues: 246 loop : -0.35 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 72 TYR 0.013 0.001 TYR B 499 PHE 0.011 0.001 PHE A 445 TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 8275) covalent geometry : angle 0.55881 / 0.30 (11220) SS BOND : bond 0.00397 / 0.23 ( 10) SS BOND : angle 1.13960 / 0.86 ( 20) hydrogen bonds : bond 0.03430 / 2.42 ( 343) hydrogen bonds : angle 5.42060 / 3.69 ( 981) link_BETA1-4 : bond 0.00352 / 0.18 ( 2) link_BETA1-4 : angle 1.12325 / 0.54 ( 6) link_NAG-ASN : bond 0.00308 / 0.16 ( 5) link_NAG-ASN : angle 1.90868 / 1.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 339 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7076 (tptt) REVERT: B 363 TYR cc_start: 0.8525 (t80) cc_final: 0.8132 (t80) REVERT: B 528 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7358 (tt) REVERT: A 126 ASP cc_start: 0.7837 (p0) cc_final: 0.7424 (p0) REVERT: A 391 GLU cc_start: 0.6834 (pm20) cc_final: 0.6587 (pm20) REVERT: A 448 ASP cc_start: 0.8019 (m-30) cc_final: 0.7719 (m-30) REVERT: A 483 MET cc_start: 0.8220 (tpp) cc_final: 0.8003 (tpp) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.4538 time to fit residues: 52.6436 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.0570 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 529 HIS ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115517 restraints weight = 20048.682| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.03 r_work: 0.3208 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8292 Z= 0.134 Angle : 0.541 7.025 11261 Z= 0.285 Chirality : 0.043 0.245 1251 Planarity : 0.004 0.039 1411 Dihedral : 10.008 58.711 1315 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.74 % Allowed : 13.21 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.12 (0.27), residues: 972 helix: 1.76 (0.32), residues: 266 sheet: -0.72 (0.33), residues: 226 loop : -0.40 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 72 TYR 0.013 0.001 TYR B 499 PHE 0.010 0.001 PHE A 445 TRP 0.010 0.001 TRP A 398 HIS 0.003 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 8275) covalent geometry : angle 0.53572 / 0.28 (11220) SS BOND : bond 0.00313 / 0.18 ( 10) SS BOND : angle 0.96906 / 0.73 ( 20) hydrogen bonds : bond 0.03180 / 2.25 ( 343) hydrogen bonds : angle 5.28821 / 3.60 ( 981) link_BETA1-4 : bond 0.00433 / 0.22 ( 2) link_BETA1-4 : angle 1.08343 / 0.54 ( 6) link_NAG-ASN : bond 0.00314 / 0.16 ( 5) link_NAG-ASN : angle 1.87514 / 1.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 131 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7365 (ttt-90) REVERT: B 363 TYR cc_start: 0.8515 (t80) cc_final: 0.8139 (t80) REVERT: B 528 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 126 ASP cc_start: 0.7810 (p0) cc_final: 0.7371 (p0) REVERT: A 391 GLU cc_start: 0.6753 (pm20) cc_final: 0.6461 (pm20) REVERT: A 448 ASP cc_start: 0.7987 (m-30) cc_final: 0.7692 (m-30) REVERT: A 483 MET cc_start: 0.8283 (tpp) cc_final: 0.8066 (tpp) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.4097 time to fit residues: 49.8885 Evaluate side-chains 106 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 95 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 397 GLN B 529 HIS A 127 HIS A 130 GLN ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115204 restraints weight = 19197.778| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.93 r_work: 0.3204 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8292 Z= 0.144 Angle : 0.537 6.842 11261 Z= 0.283 Chirality : 0.043 0.245 1251 Planarity : 0.004 0.041 1411 Dihedral : 9.911 58.974 1315 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.74 % Allowed : 14.95 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.16 (0.27), residues: 972 helix: 1.78 (0.32), residues: 266 sheet: -0.70 (0.33), residues: 226 loop : -0.37 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 72 TYR 0.015 0.001 TYR B 499 PHE 0.010 0.001 PHE B 209 TRP 0.009 0.001 TRP A 398 HIS 0.003 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8275) covalent geometry : angle 0.53099 / 0.28 (11220) SS BOND : bond 0.00347 / 0.20 ( 10) SS BOND : angle 1.02647 / 0.78 ( 20) hydrogen bonds : bond 0.03194 / 2.25 ( 343) hydrogen bonds : angle 5.24303 / 3.57 ( 981) link_BETA1-4 : bond 0.00388 / 0.20 ( 2) link_BETA1-4 : angle 1.14193 / 0.55 ( 6) link_NAG-ASN : bond 0.00313 / 0.16 ( 5) link_NAG-ASN : angle 1.90144 / 1.67 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 131 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7324 (ttt-90) REVERT: B 363 TYR cc_start: 0.8464 (t80) cc_final: 0.8075 (t80) REVERT: B 528 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7351 (tt) REVERT: A 126 ASP cc_start: 0.7710 (p0) cc_final: 0.7250 (p0) REVERT: A 391 GLU cc_start: 0.6694 (pm20) cc_final: 0.6467 (pm20) REVERT: A 448 ASP cc_start: 0.7960 (m-30) cc_final: 0.7672 (m-30) REVERT: A 483 MET cc_start: 0.8273 (tpp) cc_final: 0.8049 (tpp) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.4225 time to fit residues: 47.4749 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 529 HIS ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114380 restraints weight = 20401.784| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.06 r_work: 0.3171 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8292 Z= 0.158 Angle : 0.553 9.246 11261 Z= 0.288 Chirality : 0.043 0.245 1251 Planarity : 0.004 0.044 1411 Dihedral : 9.908 59.491 1315 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 14.83 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.16 (0.27), residues: 972 helix: 1.76 (0.32), residues: 266 sheet: -0.71 (0.32), residues: 246 loop : -0.31 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 72 TYR 0.014 0.001 TYR B 499 PHE 0.009 0.001 PHE B 209 TRP 0.009 0.001 TRP B 398 HIS 0.004 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8275) covalent geometry : angle 0.54679 / 0.29 (11220) SS BOND : bond 0.00371 / 0.21 ( 10) SS BOND : angle 1.07120 / 0.82 ( 20) hydrogen bonds : bond 0.03214 / 2.27 ( 343) hydrogen bonds : angle 5.26449 / 3.59 ( 981) link_BETA1-4 : bond 0.00416 / 0.21 ( 2) link_BETA1-4 : angle 1.15527 / 0.55 ( 6) link_NAG-ASN : bond 0.00334 / 0.17 ( 5) link_NAG-ASN : angle 1.86077 / 1.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8480 (t80) cc_final: 0.8084 (t80) REVERT: B 528 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 126 ASP cc_start: 0.7732 (p0) cc_final: 0.7304 (p0) REVERT: A 391 GLU cc_start: 0.6692 (pm20) cc_final: 0.6434 (pm20) REVERT: A 448 ASP cc_start: 0.7958 (m-30) cc_final: 0.7694 (m-30) REVERT: A 483 MET cc_start: 0.8258 (tpp) cc_final: 0.8032 (tpp) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.4863 time to fit residues: 57.5872 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 397 GLN B 529 HIS A 130 GLN ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113205 restraints weight = 23511.061| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.28 r_work: 0.3160 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8292 Z= 0.160 Angle : 0.549 9.050 11261 Z= 0.287 Chirality : 0.043 0.245 1251 Planarity : 0.004 0.044 1411 Dihedral : 9.870 59.956 1315 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.97 % Allowed : 15.06 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.27), residues: 972 helix: 1.76 (0.32), residues: 266 sheet: -0.68 (0.31), residues: 244 loop : -0.33 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.014 0.001 TYR B 499 PHE 0.010 0.001 PHE B 209 TRP 0.009 0.001 TRP B 398 HIS 0.004 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 8275) covalent geometry : angle 0.54263 / 0.29 (11220) SS BOND : bond 0.00381 / 0.22 ( 10) SS BOND : angle 1.09233 / 0.83 ( 20) hydrogen bonds : bond 0.03231 / 2.28 ( 343) hydrogen bonds : angle 5.25595 / 3.58 ( 981) link_BETA1-4 : bond 0.00425 / 0.22 ( 2) link_BETA1-4 : angle 1.20229 / 0.59 ( 6) link_NAG-ASN : bond 0.00317 / 0.17 ( 5) link_NAG-ASN : angle 1.92160 / 1.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8531 (t80) cc_final: 0.8136 (t80) REVERT: B 528 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 126 ASP cc_start: 0.7826 (p0) cc_final: 0.7400 (p0) REVERT: A 391 GLU cc_start: 0.6770 (pm20) cc_final: 0.6507 (pm20) REVERT: A 448 ASP cc_start: 0.7988 (m-30) cc_final: 0.7739 (m-30) REVERT: A 483 MET cc_start: 0.8275 (tpp) cc_final: 0.8020 (tpp) outliers start: 15 outliers final: 11 residues processed: 107 average time/residue: 0.4307 time to fit residues: 49.4646 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115138 restraints weight = 23701.232| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.27 r_work: 0.3177 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8292 Z= 0.127 Angle : 0.532 8.431 11261 Z= 0.277 Chirality : 0.042 0.240 1251 Planarity : 0.004 0.042 1411 Dihedral : 9.785 59.826 1315 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.62 % Allowed : 15.06 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.21 (0.27), residues: 972 helix: 1.83 (0.32), residues: 268 sheet: -0.70 (0.33), residues: 226 loop : -0.34 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.014 0.001 TYR B 499 PHE 0.009 0.001 PHE B 209 TRP 0.010 0.001 TRP A 398 HIS 0.003 0.000 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8275) covalent geometry : angle 0.52641 / 0.28 (11220) SS BOND : bond 0.00268 / 0.16 ( 10) SS BOND : angle 0.88150 / 0.67 ( 20) hydrogen bonds : bond 0.03015 / 2.13 ( 343) hydrogen bonds : angle 5.14404 / 3.51 ( 981) link_BETA1-4 : bond 0.00409 / 0.21 ( 2) link_BETA1-4 : angle 1.13392 / 0.57 ( 6) link_NAG-ASN : bond 0.00330 / 0.17 ( 5) link_NAG-ASN : angle 1.87742 / 1.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8448 (t80) cc_final: 0.8059 (t80) REVERT: B 528 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 126 ASP cc_start: 0.7633 (p0) cc_final: 0.7250 (p0) REVERT: A 391 GLU cc_start: 0.6640 (pm20) cc_final: 0.6400 (pm20) REVERT: A 448 ASP cc_start: 0.7908 (m-30) cc_final: 0.7658 (m-30) REVERT: A 483 MET cc_start: 0.8237 (tpp) cc_final: 0.7985 (tpp) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.4226 time to fit residues: 49.5999 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.0370 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 397 GLN ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115571 restraints weight = 19495.086| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.97 r_work: 0.3210 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8292 Z= 0.138 Angle : 0.542 8.489 11261 Z= 0.281 Chirality : 0.043 0.241 1251 Planarity : 0.004 0.044 1411 Dihedral : 9.737 59.798 1315 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 14.95 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 972 helix: 1.83 (0.32), residues: 268 sheet: -0.73 (0.32), residues: 226 loop : -0.33 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 131 TYR 0.014 0.001 TYR B 499 PHE 0.010 0.001 PHE B 209 TRP 0.009 0.001 TRP A 398 HIS 0.003 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8275) covalent geometry : angle 0.53633 / 0.28 (11220) SS BOND : bond 0.00316 / 0.18 ( 10) SS BOND : angle 0.97657 / 0.75 ( 20) hydrogen bonds : bond 0.03049 / 2.15 ( 343) hydrogen bonds : angle 5.12925 / 3.50 ( 981) link_BETA1-4 : bond 0.00405 / 0.21 ( 2) link_BETA1-4 : angle 1.13361 / 0.55 ( 6) link_NAG-ASN : bond 0.00312 / 0.16 ( 5) link_NAG-ASN : angle 1.91933 / 1.68 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 363 TYR cc_start: 0.8527 (t80) cc_final: 0.8055 (t80) REVERT: B 528 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 126 ASP cc_start: 0.7660 (p0) cc_final: 0.7248 (p0) REVERT: A 391 GLU cc_start: 0.6683 (pm20) cc_final: 0.6449 (pm20) REVERT: A 448 ASP cc_start: 0.7895 (m-30) cc_final: 0.7652 (m-30) REVERT: A 483 MET cc_start: 0.8243 (tpp) cc_final: 0.7993 (tpp) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.4003 time to fit residues: 46.0150 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 397 GLN ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115296 restraints weight = 22736.839| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.21 r_work: 0.3189 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8292 Z= 0.134 Angle : 0.543 8.205 11261 Z= 0.282 Chirality : 0.043 0.240 1251 Planarity : 0.004 0.045 1411 Dihedral : 9.718 59.955 1315 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.39 % Allowed : 15.53 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.21 (0.27), residues: 972 helix: 1.86 (0.32), residues: 268 sheet: -0.75 (0.32), residues: 226 loop : -0.31 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 72 TYR 0.014 0.001 TYR B 499 PHE 0.010 0.001 PHE B 209 TRP 0.009 0.001 TRP A 398 HIS 0.003 0.000 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 8275) covalent geometry : angle 0.53720 / 0.28 (11220) SS BOND : bond 0.00296 / 0.17 ( 10) SS BOND : angle 0.95363 / 0.72 ( 20) hydrogen bonds : bond 0.03022 / 2.13 ( 343) hydrogen bonds : angle 5.12376 / 3.51 ( 981) link_BETA1-4 : bond 0.00378 / 0.19 ( 2) link_BETA1-4 : angle 1.10637 / 0.53 ( 6) link_NAG-ASN : bond 0.00324 / 0.17 ( 5) link_NAG-ASN : angle 1.87984 / 1.66 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.24 seconds wall clock time: 39 minutes 47.93 seconds (2387.93 seconds total)