Starting phenix.real_space_refine on Tue Mar 3 17:55:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjl_51396/03_2026/9gjl_51396.map" } resolution = 3.4 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= 0.002 sd= 0.097 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 69 5.16 5 C 4705 2.51 5 N 1266 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7559 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 5113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5113 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 17, 'TRANS': 628} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'GAL': 1, 'NDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" 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 Time building chain proxies: 1.84, per 1000 atoms: 0.24 Number of scatterers: 7559 At special positions: 0 Unit cell: (99.008, 94.016, 112.32, 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 69 16.00 O 1519 8.00 N 1266 7.00 C 4705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.04 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.04 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.04 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.02 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NDG C 1 " - " GAL C 2 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG H 701 " - " ASN H 468 " " NAG H 702 " - " ASN H 198 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 232.1 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 21 sheets defined 17.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.900A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 196 removed outlier: 4.033A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 235 removed outlier: 3.672A pdb=" N ILE H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS H 229 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 273 Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 328 through 334 Processing helix chain 'H' and resid 350 through 359 removed outlier: 3.645A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG H 359 " --> pdb=" O ARG H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 586 through 590 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.575A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 138 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 removed outlier: 3.528A pdb=" N THR L 225 " --> pdb=" O LYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 258 removed outlier: 3.945A pdb=" N LYS L 258 " --> pdb=" O THR L 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.637A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.637A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262 removed outlier: 6.037A pdb=" N THR H 214 " --> pdb=" O LYS H 245 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL H 247 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU H 249 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 218 " --> pdb=" O LEU H 249 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE H 220 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS H 215 " --> pdb=" O ARG H 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR H 314 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 426 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456 removed outlier: 6.734A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 479 through 481 Processing sheet with id=AA8, first strand: chain 'H' and resid 511 through 515 removed outlier: 6.462A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 572 Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 removed outlier: 4.222A pdb=" N LYS H 602 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 630 Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.261A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB7, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AB8, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AB9, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.703A pdb=" N THR L 149 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 156 through 160 Processing sheet with id=AC2, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC3, first strand: chain 'L' and resid 207 through 212 224 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.04 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: 2420 1.34 - 1.46: 1886 1.46 - 1.58: 3324 1.58 - 1.71: 0 1.71 - 1.83: 85 Bond restraints: 7715 Sorted by residual: bond pdb=" CB CYS H 515 " pdb=" SG CYS H 515 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.04e+00 bond pdb=" CA GLU H 547 " pdb=" CB GLU H 547 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.78e-02 3.16e+03 1.04e+00 bond pdb=" N CYS H 515 " pdb=" CA CYS H 515 " ideal model delta sigma weight residual 1.454 1.442 0.012 1.19e-02 7.06e+03 1.02e+00 bond pdb=" CB CYS H 477 " pdb=" SG CYS H 477 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.36e-01 bond pdb=" CA THR H 470 " pdb=" CB THR H 470 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.70e-02 3.46e+03 7.09e-01 ... (remaining 7710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 10309 2.01 - 4.02: 108 4.02 - 6.03: 17 6.03 - 8.05: 4 8.05 - 10.06: 1 Bond angle restraints: 10439 Sorted by residual: angle pdb=" CA GLU H 547 " pdb=" CB GLU H 547 " pdb=" CG GLU H 547 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CB MET H 531 " pdb=" CG MET H 531 " pdb=" SD MET H 531 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N THR H 470 " pdb=" CA THR H 470 " pdb=" C THR H 470 " ideal model delta sigma weight residual 111.30 115.81 -4.51 1.36e+00 5.41e-01 1.10e+01 angle pdb=" C ASP H 469 " pdb=" N THR H 470 " pdb=" CA THR H 470 " ideal model delta sigma weight residual 122.46 126.72 -4.26 1.41e+00 5.03e-01 9.15e+00 angle pdb=" CA CYS H 492 " pdb=" CB CYS H 492 " pdb=" SG CYS H 492 " ideal model delta sigma weight residual 114.40 120.88 -6.48 2.30e+00 1.89e-01 7.93e+00 ... (remaining 10434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.20: 4186 19.20 - 38.41: 573 38.41 - 57.61: 102 57.61 - 76.82: 42 76.82 - 96.02: 21 Dihedral angle restraints: 4924 sinusoidal: 2196 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS H 601 " pdb=" SG CYS H 601 " pdb=" SG CYS H 613 " pdb=" CB CYS H 613 " ideal model delta sinusoidal sigma weight residual -86.00 -7.29 -78.71 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS H 592 " pdb=" SG CYS H 592 " pdb=" SG CYS H 630 " pdb=" CB CYS H 630 " ideal model delta sinusoidal sigma weight residual -86.00 -146.39 60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS H 420 " pdb=" SG CYS H 420 " pdb=" SG CYS H 456 " pdb=" CB CYS H 456 " ideal model delta sinusoidal sigma weight residual 93.00 150.79 -57.79 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 4921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 726 0.032 - 0.064: 307 0.064 - 0.096: 82 0.096 - 0.128: 50 0.128 - 0.160: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA THR H 470 " pdb=" N THR H 470 " pdb=" C THR H 470 " pdb=" CB THR H 470 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1167 not shown) Planarity restraints: 1333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 479 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO H 480 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 480 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 480 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 364 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO H 365 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO L 40 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.021 5.00e-02 4.00e+02 ... (remaining 1330 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1279 2.77 - 3.30: 6740 3.30 - 3.83: 11844 3.83 - 4.37: 14008 4.37 - 4.90: 24751 Nonbonded interactions: 58622 Sorted by model distance: nonbonded pdb=" OG1 THR H 331 " pdb=" OE1 GLU H 332 " model vdw 2.234 3.040 nonbonded pdb=" OG SER H 512 " pdb=" OE1 GLN H 548 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR H 569 " pdb=" O CYS H 603 " model vdw 2.251 3.040 nonbonded pdb=" O CYS L 71 " pdb=" NH2 ARG L 76 " model vdw 2.277 3.120 nonbonded pdb=" OD2 ASP H 26 " pdb=" NH1 ARG H 182 " model vdw 2.318 3.120 ... (remaining 58617 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 8.600 Find NCS groups from input model: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.047 7754 Z= 0.118 Angle : 0.566 10.056 10530 Z= 0.298 Chirality : 0.042 0.160 1170 Planarity : 0.004 0.048 1329 Dihedral : 18.420 96.021 3096 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.12 % Allowed : 23.35 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 915 helix: -0.66 (0.53), residues: 97 sheet: -0.05 (0.38), residues: 200 loop : -0.13 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 146 TYR 0.016 0.001 TYR H 467 PHE 0.015 0.001 PHE H 521 TRP 0.013 0.001 TRP L 223 HIS 0.002 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7715) covalent geometry : angle 0.54941 (10439) SS BOND : bond 0.00303 ( 26) SS BOND : angle 1.66954 ( 52) hydrogen bonds : bond 0.16585 ( 199) hydrogen bonds : angle 7.18259 ( 558) link_ALPHA1-2 : bond 0.00429 ( 2) link_ALPHA1-2 : angle 1.46737 ( 6) link_ALPHA1-3 : bond 0.00245 ( 1) link_ALPHA1-3 : angle 1.62404 ( 3) link_ALPHA1-6 : bond 0.00340 ( 1) link_ALPHA1-6 : angle 1.37349 ( 3) link_BETA1-4 : bond 0.00334 ( 5) link_BETA1-4 : angle 1.63833 ( 15) link_NAG-ASN : bond 0.00122 ( 4) link_NAG-ASN : angle 1.13763 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.0951 time to fit residues: 11.9129 Evaluate side-chains 81 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN L 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.192901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137585 restraints weight = 8512.088| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.04 r_work: 0.3220 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7754 Z= 0.229 Angle : 0.632 6.328 10530 Z= 0.323 Chirality : 0.047 0.203 1170 Planarity : 0.004 0.042 1329 Dihedral : 10.723 76.258 1303 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.25 % Allowed : 21.54 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 915 helix: -0.15 (0.53), residues: 98 sheet: -0.29 (0.37), residues: 199 loop : -0.27 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 146 TYR 0.012 0.002 TYR H 28 PHE 0.020 0.002 PHE H 64 TRP 0.015 0.002 TRP L 223 HIS 0.005 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 7715) covalent geometry : angle 0.61435 (10439) SS BOND : bond 0.00302 ( 26) SS BOND : angle 1.35005 ( 52) hydrogen bonds : bond 0.03949 ( 199) hydrogen bonds : angle 5.93005 ( 558) link_ALPHA1-2 : bond 0.00461 ( 2) link_ALPHA1-2 : angle 1.46764 ( 6) link_ALPHA1-3 : bond 0.00457 ( 1) link_ALPHA1-3 : angle 1.45826 ( 3) link_ALPHA1-6 : bond 0.00038 ( 1) link_ALPHA1-6 : angle 1.78715 ( 3) link_BETA1-4 : bond 0.00389 ( 5) link_BETA1-4 : angle 2.57673 ( 15) link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 1.98114 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (p0) REVERT: H 523 LYS cc_start: 0.7491 (tptt) cc_final: 0.7180 (pttp) REVERT: L 102 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.6977 (mmm160) outliers start: 27 outliers final: 16 residues processed: 111 average time/residue: 0.0920 time to fit residues: 13.7102 Evaluate side-chains 101 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 0.0040 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.196730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142450 restraints weight = 8447.937| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.93 r_work: 0.3301 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7754 Z= 0.097 Angle : 0.537 7.332 10530 Z= 0.273 Chirality : 0.044 0.194 1170 Planarity : 0.003 0.039 1329 Dihedral : 9.082 61.690 1301 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.01 % Allowed : 22.26 % Favored : 74.73 % 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: -0.23 (0.28), residues: 915 helix: 0.08 (0.55), residues: 103 sheet: -0.03 (0.40), residues: 179 loop : -0.17 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 273 TYR 0.008 0.001 TYR H 50 PHE 0.014 0.001 PHE H 258 TRP 0.013 0.001 TRP L 223 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7715) covalent geometry : angle 0.52179 (10439) SS BOND : bond 0.00263 ( 26) SS BOND : angle 0.97073 ( 52) hydrogen bonds : bond 0.03186 ( 199) hydrogen bonds : angle 5.52447 ( 558) link_ALPHA1-2 : bond 0.00417 ( 2) link_ALPHA1-2 : angle 1.52106 ( 6) link_ALPHA1-3 : bond 0.00919 ( 1) link_ALPHA1-3 : angle 1.52379 ( 3) link_ALPHA1-6 : bond 0.00068 ( 1) link_ALPHA1-6 : angle 1.88142 ( 3) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 2.36883 ( 15) link_NAG-ASN : bond 0.00341 ( 4) link_NAG-ASN : angle 1.60972 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 137 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6286 (pttm) REVERT: H 154 ASN cc_start: 0.8850 (p0) cc_final: 0.8634 (p0) REVERT: H 264 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8395 (tp) REVERT: H 523 LYS cc_start: 0.7232 (tptt) cc_final: 0.6832 (pttp) REVERT: L 102 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.6965 (mmm-85) REVERT: L 145 TYR cc_start: 0.8290 (m-80) cc_final: 0.8024 (m-80) outliers start: 25 outliers final: 12 residues processed: 106 average time/residue: 0.0944 time to fit residues: 13.5251 Evaluate side-chains 99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 530 GLU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 ASN L 138 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.187298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131672 restraints weight = 8668.430| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.13 r_work: 0.3185 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7754 Z= 0.231 Angle : 0.624 6.625 10530 Z= 0.319 Chirality : 0.047 0.279 1170 Planarity : 0.004 0.041 1329 Dihedral : 8.133 58.768 1301 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.09 % Allowed : 22.50 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 915 helix: 0.20 (0.57), residues: 92 sheet: -0.30 (0.38), residues: 189 loop : -0.29 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 280 TYR 0.013 0.002 TYR H 166 PHE 0.020 0.002 PHE H 258 TRP 0.015 0.002 TRP L 223 HIS 0.005 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 7715) covalent geometry : angle 0.60297 (10439) SS BOND : bond 0.00340 ( 26) SS BOND : angle 1.52986 ( 52) hydrogen bonds : bond 0.03709 ( 199) hydrogen bonds : angle 5.65972 ( 558) link_ALPHA1-2 : bond 0.00361 ( 2) link_ALPHA1-2 : angle 1.53353 ( 6) link_ALPHA1-3 : bond 0.00349 ( 1) link_ALPHA1-3 : angle 1.69369 ( 3) link_ALPHA1-6 : bond 0.00003 ( 1) link_ALPHA1-6 : angle 1.75989 ( 3) link_BETA1-4 : bond 0.00363 ( 5) link_BETA1-4 : angle 2.68776 ( 15) link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 1.99150 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8746 (p0) REVERT: H 425 CYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7219 (t) REVERT: H 515 CYS cc_start: 0.6847 (t) cc_final: 0.6573 (t) REVERT: H 523 LYS cc_start: 0.7227 (tptt) cc_final: 0.6744 (pttp) REVERT: H 531 MET cc_start: 0.8118 (tmm) cc_final: 0.7900 (tmm) REVERT: L 102 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.6966 (mmm160) outliers start: 34 outliers final: 24 residues processed: 114 average time/residue: 0.0868 time to fit residues: 13.7257 Evaluate side-chains 112 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 425 CYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 530 GLU Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 36 ASN Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 243 GLN Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.188845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135006 restraints weight = 8476.134| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.03 r_work: 0.3236 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7754 Z= 0.120 Angle : 0.547 8.035 10530 Z= 0.279 Chirality : 0.044 0.230 1170 Planarity : 0.003 0.040 1329 Dihedral : 7.419 50.619 1301 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.13 % Allowed : 22.86 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.28), residues: 915 helix: 0.13 (0.56), residues: 97 sheet: -0.17 (0.39), residues: 189 loop : -0.23 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 146 TYR 0.010 0.001 TYR H 27 PHE 0.016 0.001 PHE H 258 TRP 0.015 0.001 TRP L 223 HIS 0.003 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7715) covalent geometry : angle 0.53121 (10439) SS BOND : bond 0.00323 ( 26) SS BOND : angle 1.04360 ( 52) hydrogen bonds : bond 0.03120 ( 199) hydrogen bonds : angle 5.33710 ( 558) link_ALPHA1-2 : bond 0.00395 ( 2) link_ALPHA1-2 : angle 1.55894 ( 6) link_ALPHA1-3 : bond 0.00928 ( 1) link_ALPHA1-3 : angle 1.39948 ( 3) link_ALPHA1-6 : bond 0.00164 ( 1) link_ALPHA1-6 : angle 1.84214 ( 3) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.35987 ( 15) link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 1.79532 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8716 (p0) REVERT: H 264 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (tp) REVERT: H 449 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8543 (p) REVERT: H 495 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8278 (mtpt) REVERT: H 531 MET cc_start: 0.8101 (tmm) cc_final: 0.7855 (tmm) REVERT: L 102 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.6959 (mmm-85) REVERT: L 145 TYR cc_start: 0.8343 (m-80) cc_final: 0.8078 (m-80) outliers start: 26 outliers final: 16 residues processed: 102 average time/residue: 0.0842 time to fit residues: 11.9099 Evaluate side-chains 98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 530 GLU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116346 restraints weight = 8920.591| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.16 r_work: 0.3046 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 7754 Z= 0.288 Angle : 0.667 7.970 10530 Z= 0.343 Chirality : 0.048 0.201 1170 Planarity : 0.004 0.044 1329 Dihedral : 7.861 56.080 1301 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.45 % Allowed : 22.50 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 915 helix: 0.07 (0.57), residues: 92 sheet: -0.64 (0.37), residues: 198 loop : -0.46 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 280 TYR 0.015 0.002 TYR H 166 PHE 0.021 0.002 PHE H 64 TRP 0.015 0.002 TRP L 223 HIS 0.005 0.002 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 7715) covalent geometry : angle 0.64713 (10439) SS BOND : bond 0.00561 ( 26) SS BOND : angle 1.49492 ( 52) hydrogen bonds : bond 0.03823 ( 199) hydrogen bonds : angle 5.68844 ( 558) link_ALPHA1-2 : bond 0.00511 ( 2) link_ALPHA1-2 : angle 1.54885 ( 6) link_ALPHA1-3 : bond 0.00156 ( 1) link_ALPHA1-3 : angle 1.58433 ( 3) link_ALPHA1-6 : bond 0.00165 ( 1) link_ALPHA1-6 : angle 1.74783 ( 3) link_BETA1-4 : bond 0.00413 ( 5) link_BETA1-4 : angle 2.63529 ( 15) link_NAG-ASN : bond 0.00266 ( 4) link_NAG-ASN : angle 2.19909 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8730 (p0) REVERT: H 425 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7280 (t) REVERT: H 481 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6748 (p90) REVERT: L 102 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.6926 (mmm160) outliers start: 37 outliers final: 26 residues processed: 115 average time/residue: 0.0855 time to fit residues: 13.6760 Evaluate side-chains 112 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 425 CYS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 481 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 530 GLU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 655 ILE Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN L 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.183993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119258 restraints weight = 8752.588| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.15 r_work: 0.3108 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7754 Z= 0.112 Angle : 0.553 8.524 10530 Z= 0.282 Chirality : 0.044 0.192 1170 Planarity : 0.003 0.044 1329 Dihedral : 6.734 44.515 1301 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.49 % Allowed : 23.59 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.28), residues: 915 helix: 0.08 (0.57), residues: 97 sheet: -0.30 (0.38), residues: 189 loop : -0.32 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 146 TYR 0.010 0.001 TYR H 27 PHE 0.016 0.001 PHE H 258 TRP 0.014 0.001 TRP L 223 HIS 0.002 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7715) covalent geometry : angle 0.53370 (10439) SS BOND : bond 0.00311 ( 26) SS BOND : angle 1.37969 ( 52) hydrogen bonds : bond 0.02966 ( 199) hydrogen bonds : angle 5.28014 ( 558) link_ALPHA1-2 : bond 0.00415 ( 2) link_ALPHA1-2 : angle 1.55536 ( 6) link_ALPHA1-3 : bond 0.00998 ( 1) link_ALPHA1-3 : angle 1.21559 ( 3) link_ALPHA1-6 : bond 0.00272 ( 1) link_ALPHA1-6 : angle 1.77518 ( 3) link_BETA1-4 : bond 0.00541 ( 5) link_BETA1-4 : angle 2.26831 ( 15) link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 1.89917 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8718 (p0) REVERT: H 264 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8111 (tp) REVERT: H 332 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: H 449 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8548 (p) REVERT: H 495 LYS cc_start: 0.8765 (mtpp) cc_final: 0.7840 (mtpp) REVERT: L 102 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.6944 (mmm-85) REVERT: L 145 TYR cc_start: 0.8331 (m-80) cc_final: 0.8002 (m-80) outliers start: 29 outliers final: 18 residues processed: 104 average time/residue: 0.0899 time to fit residues: 12.8663 Evaluate side-chains 103 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 190 PHE Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN L 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.184429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119429 restraints weight = 8807.984| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.18 r_work: 0.3113 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7754 Z= 0.111 Angle : 0.546 8.627 10530 Z= 0.278 Chirality : 0.044 0.178 1170 Planarity : 0.003 0.042 1329 Dihedral : 6.294 45.894 1301 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.89 % Allowed : 23.71 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.28), residues: 915 helix: 0.18 (0.57), residues: 97 sheet: -0.50 (0.37), residues: 198 loop : -0.23 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 146 TYR 0.009 0.001 TYR H 28 PHE 0.016 0.001 PHE H 258 TRP 0.011 0.001 TRP L 223 HIS 0.002 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7715) covalent geometry : angle 0.52944 (10439) SS BOND : bond 0.00268 ( 26) SS BOND : angle 1.18353 ( 52) hydrogen bonds : bond 0.02905 ( 199) hydrogen bonds : angle 5.13523 ( 558) link_ALPHA1-2 : bond 0.00384 ( 2) link_ALPHA1-2 : angle 1.50098 ( 6) link_ALPHA1-3 : bond 0.00954 ( 1) link_ALPHA1-3 : angle 1.48383 ( 3) link_ALPHA1-6 : bond 0.00388 ( 1) link_ALPHA1-6 : angle 1.67113 ( 3) link_BETA1-4 : bond 0.00500 ( 5) link_BETA1-4 : angle 2.17906 ( 15) link_NAG-ASN : bond 0.00252 ( 4) link_NAG-ASN : angle 1.74690 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 154 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8656 (p0) REVERT: H 264 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8073 (tp) REVERT: H 332 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: H 425 CYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7147 (t) REVERT: H 449 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8600 (p) REVERT: H 511 TRP cc_start: 0.7847 (m100) cc_final: 0.7078 (m100) REVERT: L 102 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.6950 (mmm-85) REVERT: L 145 TYR cc_start: 0.8331 (m-80) cc_final: 0.7995 (m-80) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.0895 time to fit residues: 13.5657 Evaluate side-chains 106 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 425 CYS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.183349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118434 restraints weight = 8734.368| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.13 r_work: 0.3097 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7754 Z= 0.144 Angle : 0.576 8.880 10530 Z= 0.294 Chirality : 0.045 0.176 1170 Planarity : 0.004 0.043 1329 Dihedral : 6.296 46.461 1301 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.01 % Allowed : 23.23 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.28), residues: 915 helix: 0.08 (0.54), residues: 103 sheet: -0.53 (0.37), residues: 200 loop : -0.28 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 146 TYR 0.020 0.001 TYR H 481 PHE 0.017 0.001 PHE H 258 TRP 0.017 0.001 TRP L 223 HIS 0.003 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7715) covalent geometry : angle 0.55732 (10439) SS BOND : bond 0.00242 ( 26) SS BOND : angle 1.49803 ( 52) hydrogen bonds : bond 0.02970 ( 199) hydrogen bonds : angle 5.13252 ( 558) link_ALPHA1-2 : bond 0.00360 ( 2) link_ALPHA1-2 : angle 1.48246 ( 6) link_ALPHA1-3 : bond 0.00817 ( 1) link_ALPHA1-3 : angle 1.40456 ( 3) link_ALPHA1-6 : bond 0.00362 ( 1) link_ALPHA1-6 : angle 1.66264 ( 3) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 2.19293 ( 15) link_NAG-ASN : bond 0.00247 ( 4) link_NAG-ASN : angle 1.75453 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 137 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6038 (pttm) REVERT: H 154 ASN cc_start: 0.8986 (OUTLIER) cc_final: 0.8684 (p0) REVERT: H 264 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8052 (tp) REVERT: H 332 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: H 425 CYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7154 (t) REVERT: H 511 TRP cc_start: 0.7846 (m100) cc_final: 0.7085 (m100) REVERT: L 102 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.6891 (mmm-85) REVERT: L 145 TYR cc_start: 0.8340 (m-80) cc_final: 0.8009 (m-80) outliers start: 25 outliers final: 18 residues processed: 102 average time/residue: 0.0898 time to fit residues: 12.6644 Evaluate side-chains 108 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 425 CYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 71 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.185223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119850 restraints weight = 8827.577| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.18 r_work: 0.3120 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7754 Z= 0.103 Angle : 0.555 8.742 10530 Z= 0.283 Chirality : 0.043 0.181 1170 Planarity : 0.003 0.042 1329 Dihedral : 5.960 53.421 1301 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.41 % Allowed : 23.83 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 915 helix: 0.38 (0.57), residues: 97 sheet: -0.41 (0.38), residues: 197 loop : -0.28 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 146 TYR 0.011 0.001 TYR L 226 PHE 0.015 0.001 PHE H 258 TRP 0.015 0.001 TRP L 223 HIS 0.004 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7715) covalent geometry : angle 0.53793 (10439) SS BOND : bond 0.00218 ( 26) SS BOND : angle 1.39267 ( 52) hydrogen bonds : bond 0.02688 ( 199) hydrogen bonds : angle 5.01951 ( 558) link_ALPHA1-2 : bond 0.00365 ( 2) link_ALPHA1-2 : angle 1.49695 ( 6) link_ALPHA1-3 : bond 0.01094 ( 1) link_ALPHA1-3 : angle 1.35449 ( 3) link_ALPHA1-6 : bond 0.00497 ( 1) link_ALPHA1-6 : angle 1.58472 ( 3) link_BETA1-4 : bond 0.00518 ( 5) link_BETA1-4 : angle 2.06373 ( 15) link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 1.65394 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 137 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6032 (pttm) REVERT: H 154 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8655 (p0) REVERT: H 264 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7996 (tp) REVERT: H 332 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: H 511 TRP cc_start: 0.7777 (m100) cc_final: 0.7056 (m100) REVERT: H 523 LYS cc_start: 0.7043 (tptm) cc_final: 0.6693 (pttp) REVERT: L 102 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.6982 (mmm-85) REVERT: L 145 TYR cc_start: 0.8304 (m-80) cc_final: 0.7977 (m-80) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.0934 time to fit residues: 12.1812 Evaluate side-chains 100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 ASP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 266 GLN Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 332 GLU Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 415 CYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 552 VAL Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 102 ARG Chi-restraints excluded: chain L residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116464 restraints weight = 8774.153| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.15 r_work: 0.3071 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7754 Z= 0.193 Angle : 0.605 8.925 10530 Z= 0.309 Chirality : 0.045 0.177 1170 Planarity : 0.004 0.044 1329 Dihedral : 6.446 46.891 1301 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.13 % Allowed : 23.10 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.28), residues: 915 helix: 0.33 (0.55), residues: 98 sheet: -0.62 (0.37), residues: 200 loop : -0.38 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 146 TYR 0.013 0.001 TYR L 226 PHE 0.019 0.002 PHE H 258 TRP 0.016 0.002 TRP L 223 HIS 0.004 0.001 HIS H 44 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7715) covalent geometry : angle 0.58636 (10439) SS BOND : bond 0.00236 ( 26) SS BOND : angle 1.49215 ( 52) hydrogen bonds : bond 0.03199 ( 199) hydrogen bonds : angle 5.28029 ( 558) link_ALPHA1-2 : bond 0.00340 ( 2) link_ALPHA1-2 : angle 1.50063 ( 6) link_ALPHA1-3 : bond 0.00578 ( 1) link_ALPHA1-3 : angle 1.57711 ( 3) link_ALPHA1-6 : bond 0.00251 ( 1) link_ALPHA1-6 : angle 1.65636 ( 3) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 2.28455 ( 15) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.88347 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.73 seconds wall clock time: 35 minutes 46.64 seconds (2146.64 seconds total)