Starting phenix.real_space_refine on Thu Jul 2 07:18:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2026/8hc7_34654.map" } resolution = 4.54 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= 0.001 sd= 0.049 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 29 5.16 5 C 4730 2.51 5 N 1229 2.21 5 O 1385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 7373 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3480 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 24, 'TRANS': 405} Chain breaks: 6 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2134 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "H" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 793 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.28, per 1000 atoms: 0.17 Number of scatterers: 7373 At special positions: 0 Unit cell: (95.7, 105.6, 132, 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 29 16.00 O 1385 8.00 N 1229 7.00 C 4730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 343 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 417.7 milliseconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 19 sheets defined 6.7% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.838A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.895A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.388A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.685A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.563A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.849A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.513A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.039A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.994A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.668A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.836A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 403 removed outlier: 3.718A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.652A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.569A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.258A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.098A pdb=" N GLY H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 93 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 98 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 50 " --> pdb=" O PHE H 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.098A pdb=" N GLY H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 93 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU H 99 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLU L 106 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.792A pdb=" N GLN L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 37 " --> pdb=" O GLN L 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.877A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.750A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 321 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: 0.85 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2333 1.34 - 1.46: 1956 1.46 - 1.58: 3240 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 7562 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 7557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10084 1.97 - 3.94: 163 3.94 - 5.91: 27 5.91 - 7.88: 2 7.88 - 9.84: 2 Bond angle restraints: 10278 Sorted by residual: angle pdb=" CA PHE C 79 " pdb=" CB PHE C 79 " pdb=" CG PHE C 79 " ideal model delta sigma weight residual 113.80 116.84 -3.04 1.00e+00 1.00e+00 9.27e+00 angle pdb=" C PHE C 79 " pdb=" CA PHE C 79 " pdb=" CB PHE C 79 " ideal model delta sigma weight residual 111.97 117.85 -5.88 1.99e+00 2.53e-01 8.74e+00 angle pdb=" CB GLN L 38 " pdb=" CG GLN L 38 " pdb=" CD GLN L 38 " ideal model delta sigma weight residual 112.60 117.38 -4.78 1.70e+00 3.46e-01 7.92e+00 angle pdb=" CA LEU L 95 " pdb=" CB LEU L 95 " pdb=" CG LEU L 95 " ideal model delta sigma weight residual 116.30 126.14 -9.84 3.50e+00 8.16e-02 7.91e+00 angle pdb=" C PHE A 374 " pdb=" N PHE A 375 " pdb=" CA PHE A 375 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.62e+00 ... (remaining 10273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 3917 16.66 - 33.31: 375 33.31 - 49.97: 84 49.97 - 66.63: 11 66.63 - 83.28: 10 Dihedral angle restraints: 4397 sinusoidal: 1727 harmonic: 2670 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -152.66 66.66 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 39.64 53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 51.05 41.95 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 4394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 697 0.032 - 0.065: 283 0.065 - 0.097: 102 0.097 - 0.130: 51 0.130 - 0.162: 7 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1137 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.021 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP H 47 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 79 " -0.014 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE C 79 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 79 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 79 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 79 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 79 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 79 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 79 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C PHE C 79 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE C 79 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 80 " 0.008 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1565 2.78 - 3.31: 6064 3.31 - 3.84: 11596 3.84 - 4.37: 12460 4.37 - 4.90: 21732 Nonbonded interactions: 53417 Sorted by model distance: nonbonded pdb=" O ASP H 89 " pdb=" OH TYR H 93 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O ASN A 360 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.353 3.040 nonbonded pdb=" O PRO C 57 " pdb=" OG SER C 60 " model vdw 2.370 3.040 ... (remaining 53412 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.130 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 0.040 7581 Z= 0.140 Angle : 0.609 9.844 10323 Z= 0.296 Chirality : 0.045 0.162 1140 Planarity : 0.004 0.033 1317 Dihedral : 13.421 83.284 2653 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.52 (0.26), residues: 899 helix: -3.58 (0.53), residues: 31 sheet: 0.67 (0.42), residues: 168 loop : -1.44 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.014 0.001 TYR L 49 PHE 0.047 0.001 PHE C 79 TRP 0.048 0.001 TRP H 47 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 7562) covalent geometry : angle 0.60762 / 0.30 (10278) SS BOND : bond 0.00170 / 0.08 ( 12) SS BOND : angle 0.52298 / 0.29 ( 24) hydrogen bonds : bond 0.31641 / 21.95 ( 106) hydrogen bonds : angle 11.57568 / 8.10 ( 321) link_NAG-ASN : bond 0.00335 / 0.17 ( 7) link_NAG-ASN : angle 1.22643 / 0.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 58 PHE cc_start: 0.7493 (m-10) cc_final: 0.6939 (m-10) REVERT: H 84 SER cc_start: 0.7169 (p) cc_final: 0.6900 (p) REVERT: L 104 LYS cc_start: 0.4952 (tptt) cc_final: 0.4743 (tppt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0731 time to fit residues: 6.3310 Evaluate side-chains 37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 HIS C 481 ASN A 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.106572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085550 restraints weight = 36915.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085436 restraints weight = 27164.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.086971 restraints weight = 20126.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086890 restraints weight = 14224.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086954 restraints weight = 14890.762| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7581 Z= 0.128 Angle : 0.524 6.384 10323 Z= 0.267 Chirality : 0.042 0.159 1140 Planarity : 0.004 0.044 1317 Dihedral : 3.473 20.292 1006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.27), residues: 899 helix: -3.31 (0.59), residues: 37 sheet: 0.89 (0.42), residues: 179 loop : -1.17 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 158 TYR 0.028 0.001 TYR H 52 PHE 0.013 0.001 PHE A 559 TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7562) covalent geometry : angle 0.52121 / 0.27 (10278) SS BOND : bond 0.00287 / 0.18 ( 12) SS BOND : angle 0.81107 / 0.53 ( 24) hydrogen bonds : bond 0.04493 / 3.28 ( 106) hydrogen bonds : angle 7.15644 / 5.04 ( 321) link_NAG-ASN : bond 0.00276 / 0.17 ( 7) link_NAG-ASN : angle 1.20401 / 0.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.8299 (tmm160) cc_final: 0.7949 (ptp-170) REVERT: A 448 ASN cc_start: 0.7917 (t0) cc_final: 0.6979 (m-40) REVERT: A 586 ASP cc_start: 0.6395 (t0) cc_final: 0.6173 (t0) REVERT: H 63 VAL cc_start: 0.7023 (m) cc_final: 0.6731 (m) REVERT: L 3 GLN cc_start: 0.8743 (pp30) cc_final: 0.8229 (pp30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0790 time to fit residues: 6.5238 Evaluate side-chains 37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN L 37 GLN L 79 GLN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.095816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074164 restraints weight = 35400.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073506 restraints weight = 26230.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073893 restraints weight = 22471.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074075 restraints weight = 21279.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074239 restraints weight = 19164.714| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 7581 Z= 0.291 Angle : 0.764 12.272 10323 Z= 0.396 Chirality : 0.047 0.200 1140 Planarity : 0.005 0.040 1317 Dihedral : 5.016 30.840 1006 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.25 % Allowed : 6.27 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.51 (0.26), residues: 899 helix: -3.42 (0.55), residues: 37 sheet: 0.16 (0.40), residues: 182 loop : -1.28 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.034 0.003 TYR C 279 PHE 0.033 0.003 PHE C 43 TRP 0.029 0.003 TRP H 47 HIS 0.008 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.29 ( 7562) covalent geometry : angle 0.75676 / 0.39 (10278) SS BOND : bond 0.00938 / 0.57 ( 12) SS BOND : angle 1.33155 / 0.83 ( 24) hydrogen bonds : bond 0.05729 / 3.99 ( 106) hydrogen bonds : angle 7.27340 / 4.97 ( 321) link_NAG-ASN : bond 0.00445 / 0.25 ( 7) link_NAG-ASN : angle 2.15456 / 1.31 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8223 (tp) cc_final: 0.7891 (tp) REVERT: C 273 ARG cc_start: 0.3812 (ttt-90) cc_final: 0.3487 (ttt180) REVERT: A 324 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9121 (pm20) REVERT: L 3 GLN cc_start: 0.8687 (pp30) cc_final: 0.8296 (pp30) REVERT: L 89 GLN cc_start: 0.5221 (OUTLIER) cc_final: 0.4629 (tp-100) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.0820 time to fit residues: 5.9990 Evaluate side-chains 36 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 185 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.093699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.071776 restraints weight = 34201.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071314 restraints weight = 24197.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071902 restraints weight = 21139.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072079 restraints weight = 18452.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072265 restraints weight = 17418.817| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 7581 Z= 0.259 Angle : 0.696 7.638 10323 Z= 0.364 Chirality : 0.045 0.230 1140 Planarity : 0.005 0.058 1317 Dihedral : 5.111 31.620 1006 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.82 (0.26), residues: 899 helix: -3.70 (0.43), residues: 47 sheet: 0.03 (0.40), residues: 175 loop : -1.47 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 38 TYR 0.020 0.002 TYR C 279 PHE 0.022 0.002 PHE A 559 TRP 0.020 0.002 TRP H 36 HIS 0.005 0.002 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 ( 7562) covalent geometry : angle 0.68942 / 0.36 (10278) SS BOND : bond 0.00585 / 0.29 ( 12) SS BOND : angle 1.42783 / 0.91 ( 24) hydrogen bonds : bond 0.04349 / 3.13 ( 106) hydrogen bonds : angle 6.98329 / 4.79 ( 321) link_NAG-ASN : bond 0.00238 / 0.14 ( 7) link_NAG-ASN : angle 1.86042 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8166 (tmm160) cc_final: 0.7947 (ttp80) REVERT: H 93 TYR cc_start: 0.7986 (m-10) cc_final: 0.7532 (m-80) REVERT: L 3 GLN cc_start: 0.8468 (pp30) cc_final: 0.7976 (pp30) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0727 time to fit residues: 5.1611 Evaluate side-chains 31 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.096427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075839 restraints weight = 36417.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.074984 restraints weight = 31079.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.075720 restraints weight = 28739.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.075843 restraints weight = 22348.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.075913 restraints weight = 21649.465| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7581 Z= 0.118 Angle : 0.556 8.136 10323 Z= 0.283 Chirality : 0.043 0.171 1140 Planarity : 0.003 0.033 1317 Dihedral : 4.424 23.701 1006 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.27), residues: 899 helix: -3.54 (0.47), residues: 46 sheet: 0.33 (0.40), residues: 190 loop : -1.36 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.010 0.001 TYR A 489 PHE 0.011 0.001 PHE A 562 TRP 0.020 0.002 TRP H 106 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7562) covalent geometry : angle 0.54833 / 0.28 (10278) SS BOND : bond 0.00389 / 0.21 ( 12) SS BOND : angle 0.84809 / 0.55 ( 24) hydrogen bonds : bond 0.03715 / 2.65 ( 106) hydrogen bonds : angle 6.56950 / 4.54 ( 321) link_NAG-ASN : bond 0.00741 / 0.40 ( 7) link_NAG-ASN : angle 2.04487 / 1.18 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8320 (tp) cc_final: 0.8110 (tp) REVERT: H 36 TRP cc_start: 0.6757 (t-100) cc_final: 0.6552 (t-100) REVERT: H 93 TYR cc_start: 0.8074 (m-10) cc_final: 0.7602 (m-10) REVERT: L 3 GLN cc_start: 0.8328 (pp30) cc_final: 0.7882 (pp30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0782 time to fit residues: 5.4488 Evaluate side-chains 31 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.0070 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 ASN C 414 GLN A 422 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.097073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076578 restraints weight = 36492.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.075305 restraints weight = 31946.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075699 restraints weight = 31107.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076032 restraints weight = 25688.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076162 restraints weight = 23073.194| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7581 Z= 0.100 Angle : 0.536 9.482 10323 Z= 0.267 Chirality : 0.043 0.182 1140 Planarity : 0.003 0.030 1317 Dihedral : 4.103 26.653 1006 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.13 % Allowed : 2.76 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.27), residues: 899 helix: -3.56 (0.50), residues: 39 sheet: 0.64 (0.38), residues: 212 loop : -1.44 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.020 0.001 TYR C 473 PHE 0.015 0.001 PHE A 565 TRP 0.010 0.001 TRP H 106 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7562) covalent geometry : angle 0.53037 / 0.27 (10278) SS BOND : bond 0.00340 / 0.18 ( 12) SS BOND : angle 0.88159 / 0.53 ( 24) hydrogen bonds : bond 0.03417 / 2.42 ( 106) hydrogen bonds : angle 6.23491 / 4.32 ( 321) link_NAG-ASN : bond 0.00287 / 0.16 ( 7) link_NAG-ASN : angle 1.66284 / 1.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 489 TYR cc_start: 0.6236 (p90) cc_final: 0.6021 (p90) REVERT: H 36 TRP cc_start: 0.7124 (t-100) cc_final: 0.6770 (t-100) REVERT: H 73 ASN cc_start: 0.3910 (p0) cc_final: 0.3678 (p0) REVERT: L 3 GLN cc_start: 0.8400 (pp30) cc_final: 0.7925 (pp30) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.0725 time to fit residues: 4.9797 Evaluate side-chains 39 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 414 GLN ** 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 = 0.3867 r_free = 0.3867 target = 0.096101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074823 restraints weight = 33196.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.074655 restraints weight = 22923.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.075564 restraints weight = 18104.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075370 restraints weight = 16926.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075615 restraints weight = 15507.987| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7581 Z= 0.122 Angle : 0.534 7.638 10323 Z= 0.271 Chirality : 0.043 0.168 1140 Planarity : 0.003 0.027 1317 Dihedral : 4.132 23.979 1006 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.27), residues: 899 helix: -3.58 (0.49), residues: 39 sheet: 0.63 (0.39), residues: 206 loop : -1.42 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.009 0.001 TYR C 265 PHE 0.012 0.001 PHE C 79 TRP 0.008 0.001 TRP H 106 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7562) covalent geometry : angle 0.52801 / 0.27 (10278) SS BOND : bond 0.00434 / 0.22 ( 12) SS BOND : angle 1.07218 / 0.63 ( 24) hydrogen bonds : bond 0.03430 / 2.42 ( 106) hydrogen bonds : angle 6.19727 / 4.30 ( 321) link_NAG-ASN : bond 0.00259 / 0.15 ( 7) link_NAG-ASN : angle 1.60367 / 1.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8288 (tp) cc_final: 0.7927 (tp) REVERT: H 34 MET cc_start: 0.8092 (mmp) cc_final: 0.7876 (mmm) REVERT: H 73 ASN cc_start: 0.3516 (p0) cc_final: 0.3217 (p0) REVERT: L 3 GLN cc_start: 0.8535 (pp30) cc_final: 0.8240 (mm110) REVERT: L 4 MET cc_start: 0.5757 (mmp) cc_final: 0.5119 (mmp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0656 time to fit residues: 4.4230 Evaluate side-chains 34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.096728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075575 restraints weight = 33300.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.075187 restraints weight = 22747.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075804 restraints weight = 20235.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.075999 restraints weight = 17948.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076205 restraints weight = 16978.694| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7581 Z= 0.107 Angle : 0.529 7.719 10323 Z= 0.268 Chirality : 0.043 0.159 1140 Planarity : 0.003 0.029 1317 Dihedral : 4.113 26.366 1006 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.52 (0.27), residues: 899 helix: -3.29 (0.48), residues: 51 sheet: 0.58 (0.40), residues: 204 loop : -1.45 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.020 0.001 TYR C 473 PHE 0.016 0.001 PHE C 374 TRP 0.014 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7562) covalent geometry : angle 0.52389 / 0.27 (10278) SS BOND : bond 0.00371 / 0.20 ( 12) SS BOND : angle 1.00272 / 0.61 ( 24) hydrogen bonds : bond 0.03346 / 2.43 ( 106) hydrogen bonds : angle 6.35248 / 4.39 ( 321) link_NAG-ASN : bond 0.00267 / 0.16 ( 7) link_NAG-ASN : angle 1.48100 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8163 (tp) cc_final: 0.7894 (tp) REVERT: C 489 TYR cc_start: 0.6420 (p90) cc_final: 0.6159 (p90) REVERT: H 34 MET cc_start: 0.8103 (mmp) cc_final: 0.7901 (mmm) REVERT: H 59 TYR cc_start: 0.5785 (m-80) cc_final: 0.4976 (m-10) REVERT: H 73 ASN cc_start: 0.3937 (p0) cc_final: 0.3674 (p0) REVERT: L 3 GLN cc_start: 0.8566 (pp30) cc_final: 0.8276 (mm110) REVERT: L 4 MET cc_start: 0.5696 (mmp) cc_final: 0.5079 (mmp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0851 time to fit residues: 5.7083 Evaluate side-chains 37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 414 GLN ** 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 = 0.3874 r_free = 0.3874 target = 0.096544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.075377 restraints weight = 36309.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.074843 restraints weight = 27054.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075218 restraints weight = 23242.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075350 restraints weight = 21881.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.075534 restraints weight = 19618.239| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7581 Z= 0.112 Angle : 0.531 7.778 10323 Z= 0.268 Chirality : 0.043 0.162 1140 Planarity : 0.003 0.027 1317 Dihedral : 4.079 24.065 1006 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.28), residues: 899 helix: -3.13 (0.55), residues: 44 sheet: 0.56 (0.40), residues: 204 loop : -1.37 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR C 473 PHE 0.013 0.001 PHE C 79 TRP 0.016 0.001 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7562) covalent geometry : angle 0.52583 / 0.27 (10278) SS BOND : bond 0.00367 / 0.19 ( 12) SS BOND : angle 0.90585 / 0.54 ( 24) hydrogen bonds : bond 0.03349 / 2.42 ( 106) hydrogen bonds : angle 6.23669 / 4.32 ( 321) link_NAG-ASN : bond 0.00259 / 0.15 ( 7) link_NAG-ASN : angle 1.48150 / 0.95 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8177 (tp) cc_final: 0.7858 (tp) REVERT: C 489 TYR cc_start: 0.6815 (p90) cc_final: 0.6527 (p90) REVERT: H 73 ASN cc_start: 0.4232 (p0) cc_final: 0.3998 (p0) REVERT: L 3 GLN cc_start: 0.8588 (pp30) cc_final: 0.8323 (mm110) REVERT: L 4 MET cc_start: 0.5773 (mmp) cc_final: 0.5113 (mmp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0696 time to fit residues: 4.8437 Evaluate side-chains 38 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.076092 restraints weight = 36345.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076249 restraints weight = 25815.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076619 restraints weight = 21656.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076622 restraints weight = 19069.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076814 restraints weight = 17666.358| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7581 Z= 0.094 Angle : 0.529 7.848 10323 Z= 0.264 Chirality : 0.043 0.155 1140 Planarity : 0.003 0.028 1317 Dihedral : 4.005 25.408 1006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.41 (0.27), residues: 899 helix: -3.10 (0.55), residues: 44 sheet: 0.58 (0.40), residues: 204 loop : -1.39 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.009 0.001 TYR L 49 PHE 0.014 0.001 PHE C 79 TRP 0.011 0.001 TRP H 36 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 7562) covalent geometry : angle 0.52459 / 0.26 (10278) SS BOND : bond 0.00328 / 0.17 ( 12) SS BOND : angle 0.85724 / 0.52 ( 24) hydrogen bonds : bond 0.03210 / 2.31 ( 106) hydrogen bonds : angle 6.10799 / 4.26 ( 321) link_NAG-ASN : bond 0.00271 / 0.16 ( 7) link_NAG-ASN : angle 1.40341 / 0.90 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.8068 (tp) cc_final: 0.7853 (tp) REVERT: C 489 TYR cc_start: 0.6684 (p90) cc_final: 0.6285 (p90) REVERT: H 51 LEU cc_start: 0.9145 (tp) cc_final: 0.8938 (tp) REVERT: H 59 TYR cc_start: 0.6648 (m-10) cc_final: 0.6050 (m-80) REVERT: H 73 ASN cc_start: 0.4251 (p0) cc_final: 0.3997 (p0) REVERT: L 3 GLN cc_start: 0.8623 (pp30) cc_final: 0.8366 (mm110) REVERT: L 4 MET cc_start: 0.5166 (mmp) cc_final: 0.4574 (mmp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0742 time to fit residues: 5.0004 Evaluate side-chains 37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.0270 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.0770 chunk 64 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.098169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.077488 restraints weight = 36302.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077124 restraints weight = 28260.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077496 restraints weight = 24011.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077765 restraints weight = 21777.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.077943 restraints weight = 19521.747| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7581 Z= 0.086 Angle : 0.519 7.889 10323 Z= 0.259 Chirality : 0.043 0.152 1140 Planarity : 0.003 0.030 1317 Dihedral : 3.803 20.911 1006 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.13 % Allowed : 0.50 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.28), residues: 899 helix: -3.01 (0.57), residues: 44 sheet: 0.84 (0.41), residues: 193 loop : -1.40 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.008 0.001 TYR L 49 PHE 0.014 0.001 PHE C 79 TRP 0.010 0.001 TRP H 36 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 7562) covalent geometry : angle 0.51535 / 0.26 (10278) SS BOND : bond 0.00309 / 0.15 ( 12) SS BOND : angle 0.83441 / 0.50 ( 24) hydrogen bonds : bond 0.03080 / 2.19 ( 106) hydrogen bonds : angle 5.91918 / 4.16 ( 321) link_NAG-ASN : bond 0.00270 / 0.15 ( 7) link_NAG-ASN : angle 1.32956 / 0.84 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1098.51 seconds wall clock time: 19 minutes 41.99 seconds (1181.99 seconds total)