Starting phenix.real_space_refine on Sun May 11 08:31:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.map" model { file = "/net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vly_43348/05_2025/8vly_43348.cif" } resolution = 3.61 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= 0.001 sd= 0.042 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 36 5.16 5 C 5148 2.51 5 N 1217 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3834 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 23, 'TRANS': 473} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 3823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3823 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 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: "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 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.82, per 1000 atoms: 0.75 Number of scatterers: 7755 At special positions: 0 Unit cell: (87.57, 112.59, 100.914, 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 36 16.00 O 1354 8.00 N 1217 7.00 C 5148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " 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-ASN " NAG A 701 " - " ASN A 162 " " NAG A 702 " - " ASN A 94 " " NAG B 701 " - " ASN B 162 " " NAG B 702 " - " ASN B 94 " " NAG B 703 " - " ASN B 142 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.3 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 53.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 269 through 288 removed outlier: 3.609A pdb=" N GLY A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 332 removed outlier: 3.789A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.551A pdb=" N LEU A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.695A pdb=" N VAL A 371 " --> pdb=" O TRP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 417 through 438 Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.537A pdb=" N HIS A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 524 removed outlier: 4.119A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.661A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.719A pdb=" N GLY A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 632 through 657 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.655A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 332 Processing helix chain 'B' and resid 334 through 356 removed outlier: 3.534A pdb=" N LEU B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 438 removed outlier: 3.528A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.659A pdb=" N LYS B 458 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 502 through 524 removed outlier: 4.269A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 551 Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.662A pdb=" N GLY B 604 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 removed outlier: 3.631A pdb=" N HIS B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.821A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 168 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 178 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.179A pdb=" N VAL A 111 " --> pdb=" O TRP A 99 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP A 99 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 113 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 139 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG A 152 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 141 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.776A pdb=" N HIS B 87 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 167 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 132 removed outlier: 3.776A pdb=" N HIS B 87 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 167 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 115 removed outlier: 5.584A pdb=" N VAL B 111 " --> pdb=" O TRP B 99 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TRP B 99 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 113 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 96 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN B 142 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 137 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B 154 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 139 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 152 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 141 " --> pdb=" O VAL B 150 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2307 1.34 - 1.46: 1540 1.46 - 1.58: 4084 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7979 Sorted by residual: bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C TRP A 418 " pdb=" N PRO A 419 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.07e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 7974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 10615 1.38 - 2.76: 246 2.76 - 4.14: 43 4.14 - 5.52: 17 5.52 - 6.90: 5 Bond angle restraints: 10926 Sorted by residual: angle pdb=" N TRP A 418 " pdb=" CA TRP A 418 " pdb=" C TRP A 418 " ideal model delta sigma weight residual 109.81 116.05 -6.24 2.21e+00 2.05e-01 7.98e+00 angle pdb=" C LYS B 551 " pdb=" N VAL B 552 " pdb=" CA VAL B 552 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CG ARG B 269 " pdb=" CD ARG B 269 " pdb=" NE ARG B 269 " ideal model delta sigma weight residual 112.00 106.58 5.42 2.20e+00 2.07e-01 6.06e+00 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 119.42 -6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" C LEU A 268 " pdb=" N ARG A 269 " pdb=" CA ARG A 269 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.55e+00 ... (remaining 10921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4072 17.53 - 35.06: 420 35.06 - 52.59: 111 52.59 - 70.12: 21 70.12 - 87.65: 5 Dihedral angle restraints: 4629 sinusoidal: 1769 harmonic: 2860 Sorted by residual: dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 166.14 -73.14 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 462 " pdb=" CB CYS B 462 " ideal model delta sinusoidal sigma weight residual 93.00 158.41 -65.41 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sinusoidal sigma weight residual -86.00 -50.30 -35.70 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 4626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1033 0.050 - 0.100: 224 0.100 - 0.150: 30 0.150 - 0.200: 2 0.200 - 0.249: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB THR A 383 " pdb=" CA THR A 383 " pdb=" OG1 THR A 383 " pdb=" CG2 THR A 383 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CB VAL B 552 " pdb=" CA VAL B 552 " pdb=" CG1 VAL B 552 " pdb=" CG2 VAL B 552 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1287 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 269 " -0.171 9.50e-02 1.11e+02 7.69e-02 3.76e+00 pdb=" NE ARG B 269 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 269 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 269 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 269 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 269 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ARG B 269 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 269 " 0.011 2.00e-02 2.50e+03 pdb=" N SER B 270 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 274 " -0.008 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE B 274 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 274 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 274 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 274 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 274 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 274 " -0.000 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 310 2.72 - 3.27: 7942 3.27 - 3.81: 12991 3.81 - 4.36: 14477 4.36 - 4.90: 26113 Nonbonded interactions: 61833 Sorted by model distance: nonbonded pdb=" O GLU A 147 " pdb=" O6 NAG C 1 " model vdw 2.180 3.040 nonbonded pdb=" O ILE A 355 " pdb=" OH TYR A 361 " model vdw 2.204 3.040 nonbonded pdb=" NH1 ARG A 275 " pdb=" O GLY A 604 " model vdw 2.230 3.120 nonbonded pdb=" O ILE B 355 " pdb=" OH TYR B 361 " model vdw 2.245 3.040 nonbonded pdb=" O PRO A 116 " pdb=" OG SER A 125 " model vdw 2.278 3.040 ... (remaining 61828 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 76 through 144 or (resid 145 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 170 or resid 177 th \ rough 189 or resid 268 through 330 or (resid 331 and (name N or name CA or name \ C or name O or name CB )) or resid 332 through 476 or (resid 477 through 478 and \ (name N or name CA or name C or name O or name CB )) or resid 479 through 492 o \ r (resid 493 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 94 through 526 or (resid 527 and (name N or name CA or name C or name O or name \ CB )) or resid 528 through 550 or (resid 551 and (name N or name CA or name C or \ name O or name CB )) or resid 552 through 555 or (resid 556 and (name N or name \ CA or name C or name O or name CB )) or resid 557 through 660 or resid 701 thro \ ugh 702)) selection = (chain 'B' and (resid 76 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 168 or (resid 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 179 or (resid 1 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 181 through \ 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) or r \ esid 346 through 407 or resid 411 through 477 or (resid 478 and (name N or name \ CA or name C or name O or name CB )) or resid 479 through 524 or (resid 525 thro \ ugh 527 and (name N or name CA or name C or name O or name CB )) or resid 528 th \ rough 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) \ or resid 593 through 625 or (resid 626 and (name N or name CA or name C or name \ O or name CB )) or resid 627 through 655 or (resid 656 and (name N or name CA o \ r name C or name O or name CB )) or resid 657 or (resid 658 and (name N or name \ CA or name C or name O or name CB )) or resid 659 through 660 or resid 702 throu \ gh 703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.130 Find NCS groups from input model: 0.380 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.004 0.041 7993 Z= 0.161 Angle : 0.582 13.489 10961 Z= 0.286 Chirality : 0.041 0.249 1290 Planarity : 0.004 0.077 1330 Dihedral : 15.202 87.645 2780 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.38 % Allowed : 11.00 % Favored : 88.62 % 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: 1.00 (0.28), residues: 976 helix: 2.61 (0.23), residues: 465 sheet: -0.55 (0.49), residues: 122 loop : -1.44 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.007 0.001 HIS A 483 PHE 0.025 0.001 PHE B 274 TYR 0.019 0.001 TYR B 384 ARG 0.007 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 6) link_NAG-ASN : angle 4.82643 ( 18) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 1.38679 ( 3) hydrogen bonds : bond 0.12038 ( 418) hydrogen bonds : angle 5.64020 ( 1209) SS BOND : bond 0.00206 ( 7) SS BOND : angle 0.54178 ( 14) covalent geometry : bond 0.00368 ( 7979) covalent geometry : angle 0.54854 (10926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.892 Fit side-chains REVERT: A 78 LYS cc_start: 0.8777 (tppt) cc_final: 0.8542 (mmmt) REVERT: A 325 MET cc_start: 0.8374 (tmm) cc_final: 0.8040 (tmm) REVERT: A 551 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8502 (tttp) REVERT: B 269 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8284 (mtp85) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 0.2357 time to fit residues: 23.1335 Evaluate side-chains 72 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 151 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.096530 restraints weight = 12114.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099378 restraints weight = 6823.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101251 restraints weight = 4689.269| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7993 Z= 0.157 Angle : 0.571 13.132 10961 Z= 0.284 Chirality : 0.041 0.243 1290 Planarity : 0.004 0.059 1330 Dihedral : 6.167 56.579 1201 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.88 % Allowed : 12.12 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.28), residues: 976 helix: 2.58 (0.23), residues: 465 sheet: -0.63 (0.50), residues: 111 loop : -1.44 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS A 483 PHE 0.019 0.001 PHE A 601 TYR 0.018 0.001 TYR B 570 ARG 0.004 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 6) link_NAG-ASN : angle 4.68299 ( 18) link_BETA1-4 : bond 0.00623 ( 1) link_BETA1-4 : angle 1.55940 ( 3) hydrogen bonds : bond 0.03604 ( 418) hydrogen bonds : angle 4.40917 ( 1209) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.52262 ( 14) covalent geometry : bond 0.00380 ( 7979) covalent geometry : angle 0.53809 (10926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8534 (tttt) REVERT: B 269 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8511 (mtp85) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.2108 time to fit residues: 28.1730 Evaluate side-chains 86 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.0370 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097270 restraints weight = 12128.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100126 restraints weight = 6839.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102047 restraints weight = 4710.280| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7993 Z= 0.129 Angle : 0.547 13.090 10961 Z= 0.269 Chirality : 0.041 0.240 1290 Planarity : 0.003 0.027 1330 Dihedral : 5.642 57.803 1201 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.75 % Allowed : 15.62 % Favored : 81.62 % 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: 1.08 (0.28), residues: 976 helix: 2.70 (0.23), residues: 467 sheet: -0.69 (0.48), residues: 117 loop : -1.39 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.003 0.001 HIS B 87 PHE 0.018 0.001 PHE B 347 TYR 0.016 0.001 TYR B 570 ARG 0.004 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 6) link_NAG-ASN : angle 4.67593 ( 18) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 1.56098 ( 3) hydrogen bonds : bond 0.03316 ( 418) hydrogen bonds : angle 4.18795 ( 1209) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.43423 ( 14) covalent geometry : bond 0.00311 ( 7979) covalent geometry : angle 0.51298 (10926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8517 (tttt) REVERT: B 269 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8457 (mtp85) outliers start: 22 outliers final: 16 residues processed: 90 average time/residue: 0.2150 time to fit residues: 26.0490 Evaluate side-chains 83 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.116246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095318 restraints weight = 12193.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098058 restraints weight = 6868.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099943 restraints weight = 4761.143| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7993 Z= 0.176 Angle : 0.579 13.313 10961 Z= 0.287 Chirality : 0.041 0.238 1290 Planarity : 0.003 0.036 1330 Dihedral : 5.365 52.898 1200 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.50 % Allowed : 15.00 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.28), residues: 976 helix: 2.61 (0.23), residues: 467 sheet: -0.75 (0.48), residues: 118 loop : -1.40 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.004 0.001 HIS B 87 PHE 0.018 0.001 PHE A 601 TYR 0.019 0.001 TYR B 570 ARG 0.004 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 6) link_NAG-ASN : angle 4.75597 ( 18) link_BETA1-4 : bond 0.00448 ( 1) link_BETA1-4 : angle 1.52745 ( 3) hydrogen bonds : bond 0.03503 ( 418) hydrogen bonds : angle 4.22408 ( 1209) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.62258 ( 14) covalent geometry : bond 0.00428 ( 7979) covalent geometry : angle 0.54561 (10926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8531 (tttm) outliers start: 36 outliers final: 27 residues processed: 99 average time/residue: 0.1971 time to fit residues: 26.4735 Evaluate side-chains 91 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.117898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097027 restraints weight = 12028.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099830 restraints weight = 6759.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101724 restraints weight = 4654.113| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7993 Z= 0.127 Angle : 0.544 12.669 10961 Z= 0.267 Chirality : 0.040 0.237 1290 Planarity : 0.003 0.026 1330 Dihedral : 5.207 53.082 1200 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.12 % Allowed : 15.50 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.28), residues: 976 helix: 2.73 (0.23), residues: 467 sheet: -0.74 (0.48), residues: 116 loop : -1.40 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS B 87 PHE 0.016 0.001 PHE B 322 TYR 0.017 0.001 TYR B 570 ARG 0.004 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 6) link_NAG-ASN : angle 4.66381 ( 18) link_BETA1-4 : bond 0.00433 ( 1) link_BETA1-4 : angle 1.62281 ( 3) hydrogen bonds : bond 0.03243 ( 418) hydrogen bonds : angle 4.08596 ( 1209) SS BOND : bond 0.00287 ( 7) SS BOND : angle 0.59860 ( 14) covalent geometry : bond 0.00308 ( 7979) covalent geometry : angle 0.50953 (10926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7450 (m) outliers start: 33 outliers final: 27 residues processed: 101 average time/residue: 0.2079 time to fit residues: 28.6978 Evaluate side-chains 95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095775 restraints weight = 12114.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098527 restraints weight = 6809.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100393 restraints weight = 4731.602| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7993 Z= 0.163 Angle : 0.564 12.678 10961 Z= 0.279 Chirality : 0.041 0.237 1290 Planarity : 0.003 0.028 1330 Dihedral : 5.235 52.603 1200 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.38 % Allowed : 16.25 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.28), residues: 976 helix: 2.65 (0.23), residues: 467 sheet: -0.78 (0.48), residues: 116 loop : -1.43 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS B 87 PHE 0.023 0.001 PHE B 601 TYR 0.019 0.001 TYR B 570 ARG 0.007 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 6) link_NAG-ASN : angle 4.65731 ( 18) link_BETA1-4 : bond 0.00351 ( 1) link_BETA1-4 : angle 1.58541 ( 3) hydrogen bonds : bond 0.03399 ( 418) hydrogen bonds : angle 4.11232 ( 1209) SS BOND : bond 0.00254 ( 7) SS BOND : angle 0.59596 ( 14) covalent geometry : bond 0.00399 ( 7979) covalent geometry : angle 0.53104 (10926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7484 (m) outliers start: 35 outliers final: 30 residues processed: 96 average time/residue: 0.2062 time to fit residues: 27.3545 Evaluate side-chains 96 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.116464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095408 restraints weight = 12131.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098199 restraints weight = 6869.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100169 restraints weight = 4734.470| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7993 Z= 0.168 Angle : 0.572 12.580 10961 Z= 0.283 Chirality : 0.041 0.235 1290 Planarity : 0.003 0.026 1330 Dihedral : 5.271 52.457 1200 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.50 % Allowed : 16.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.28), residues: 976 helix: 2.54 (0.23), residues: 472 sheet: -0.79 (0.48), residues: 118 loop : -1.34 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS B 87 PHE 0.028 0.002 PHE B 601 TYR 0.020 0.001 TYR B 570 ARG 0.005 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 6) link_NAG-ASN : angle 4.65745 ( 18) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 1.63686 ( 3) hydrogen bonds : bond 0.03433 ( 418) hydrogen bonds : angle 4.13094 ( 1209) SS BOND : bond 0.00274 ( 7) SS BOND : angle 0.63059 ( 14) covalent geometry : bond 0.00410 ( 7979) covalent geometry : angle 0.53920 (10926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7493 (m) outliers start: 36 outliers final: 32 residues processed: 99 average time/residue: 0.1969 time to fit residues: 26.6015 Evaluate side-chains 99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 87 optimal weight: 0.0770 chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096476 restraints weight = 12306.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.099322 restraints weight = 6933.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101247 restraints weight = 4770.668| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7993 Z= 0.134 Angle : 0.549 11.974 10961 Z= 0.272 Chirality : 0.040 0.236 1290 Planarity : 0.003 0.026 1330 Dihedral : 5.192 52.608 1200 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.88 % Allowed : 17.62 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.28), residues: 976 helix: 2.71 (0.23), residues: 467 sheet: -0.78 (0.47), residues: 116 loop : -1.41 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS B 87 PHE 0.029 0.001 PHE B 601 TYR 0.017 0.001 TYR B 570 ARG 0.006 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 6) link_NAG-ASN : angle 4.53318 ( 18) link_BETA1-4 : bond 0.00466 ( 1) link_BETA1-4 : angle 1.69255 ( 3) hydrogen bonds : bond 0.03272 ( 418) hydrogen bonds : angle 4.04797 ( 1209) SS BOND : bond 0.00244 ( 7) SS BOND : angle 0.61608 ( 14) covalent geometry : bond 0.00327 ( 7979) covalent geometry : angle 0.51678 (10926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7465 (m) outliers start: 31 outliers final: 29 residues processed: 95 average time/residue: 0.1980 time to fit residues: 25.9416 Evaluate side-chains 95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 42 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.118302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097039 restraints weight = 12198.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099915 restraints weight = 6888.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101764 restraints weight = 4734.664| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7993 Z= 0.128 Angle : 0.546 11.544 10961 Z= 0.270 Chirality : 0.040 0.239 1290 Planarity : 0.003 0.026 1330 Dihedral : 5.179 52.712 1200 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.12 % Allowed : 17.62 % Favored : 78.25 % 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: 1.10 (0.28), residues: 976 helix: 2.74 (0.23), residues: 467 sheet: -0.65 (0.49), residues: 111 loop : -1.41 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS B 87 PHE 0.025 0.001 PHE B 601 TYR 0.017 0.001 TYR B 570 ARG 0.006 0.001 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 6) link_NAG-ASN : angle 4.44081 ( 18) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 1.63498 ( 3) hydrogen bonds : bond 0.03210 ( 418) hydrogen bonds : angle 3.97405 ( 1209) SS BOND : bond 0.00434 ( 7) SS BOND : angle 0.50337 ( 14) covalent geometry : bond 0.00309 ( 7979) covalent geometry : angle 0.51489 (10926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 107 CYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7467 (m) REVERT: A 551 LYS cc_start: 0.8559 (tttt) cc_final: 0.8258 (tttp) outliers start: 33 outliers final: 27 residues processed: 97 average time/residue: 0.1930 time to fit residues: 25.9213 Evaluate side-chains 96 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 88 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.118182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096987 restraints weight = 12148.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099812 restraints weight = 6881.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101778 restraints weight = 4753.762| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7993 Z= 0.130 Angle : 0.550 10.827 10961 Z= 0.272 Chirality : 0.040 0.239 1290 Planarity : 0.003 0.026 1330 Dihedral : 5.140 52.633 1200 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.62 % Allowed : 17.88 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.28), residues: 976 helix: 2.74 (0.23), residues: 467 sheet: -0.67 (0.49), residues: 111 loop : -1.37 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS B 87 PHE 0.020 0.001 PHE B 601 TYR 0.016 0.001 TYR B 570 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 6) link_NAG-ASN : angle 4.31072 ( 18) link_BETA1-4 : bond 0.00253 ( 1) link_BETA1-4 : angle 1.59312 ( 3) hydrogen bonds : bond 0.03192 ( 418) hydrogen bonds : angle 3.97052 ( 1209) SS BOND : bond 0.00272 ( 7) SS BOND : angle 0.75143 ( 14) covalent geometry : bond 0.00313 ( 7979) covalent geometry : angle 0.52119 (10926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.901 Fit side-chains REVERT: A 107 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7480 (m) REVERT: A 317 MET cc_start: 0.8202 (tmm) cc_final: 0.7922 (ttp) REVERT: A 551 LYS cc_start: 0.8555 (tttt) cc_final: 0.8240 (tttp) outliers start: 29 outliers final: 27 residues processed: 95 average time/residue: 0.2169 time to fit residues: 27.8713 Evaluate side-chains 97 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 88 optimal weight: 0.0670 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.118883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097656 restraints weight = 12190.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.100521 restraints weight = 6911.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102483 restraints weight = 4760.082| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7993 Z= 0.118 Angle : 0.553 13.623 10961 Z= 0.269 Chirality : 0.040 0.241 1290 Planarity : 0.003 0.033 1330 Dihedral : 5.089 52.624 1200 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.50 % Allowed : 17.62 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.28), residues: 976 helix: 2.78 (0.23), residues: 467 sheet: -0.63 (0.49), residues: 111 loop : -1.35 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.003 0.001 HIS B 87 PHE 0.017 0.001 PHE B 322 TYR 0.015 0.001 TYR B 570 ARG 0.006 0.001 ARG B 534 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 6) link_NAG-ASN : angle 4.96888 ( 18) link_BETA1-4 : bond 0.00388 ( 1) link_BETA1-4 : angle 1.60386 ( 3) hydrogen bonds : bond 0.03088 ( 418) hydrogen bonds : angle 3.93148 ( 1209) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.52470 ( 14) covalent geometry : bond 0.00283 ( 7979) covalent geometry : angle 0.51448 (10926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2422.06 seconds wall clock time: 43 minutes 19.30 seconds (2599.30 seconds total)