Starting phenix.real_space_refine on Tue Mar 3 17:51:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.map" model { file = "/net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gja_51385/03_2026/9gja_51385.cif" } resolution = 3.7 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= 0.099 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 4702 2.51 5 N 1265 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 7551 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 5103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5103 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 17, 'TRANS': 627} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 1.88, per 1000 atoms: 0.25 Number of scatterers: 7551 At special positions: 0 Unit cell: (94.848, 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 1515 8.00 N 1265 7.00 C 4702 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=2.04 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=2.03 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=2.03 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=2.03 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=2.03 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 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG C 1 " - " ASN H 468 " " NAG H 701 " - " ASN H 95 " " NAG H 702 " - " ASN H 198 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 299.5 milliseconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 15.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.919A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.881A pdb=" N ILE H 129 " --> pdb=" O GLU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 196 removed outlier: 3.736A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 235 removed outlier: 4.546A pdb=" N LYS H 229 " --> pdb=" O SER H 225 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.540A pdb=" N GLN H 240 " --> pdb=" O LEU H 237 " (cutoff:3.500A) 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 298 Processing helix chain 'H' and resid 328 through 333 removed outlier: 3.795A pdb=" N PHE H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.696A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (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 604 through 608 Processing helix chain 'L' and resid 92 through 99 removed outlier: 3.682A pdb=" N LYS L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 138 removed outlier: 3.673A pdb=" N GLN L 138 " --> pdb=" O ASN L 135 " (cutoff:3.500A) No H-bonds generated for '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 Processing sheet with id=AA1, first strand: chain 'H' and resid 106 through 108 removed outlier: 3.957A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY H 36 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP H 29 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR H 180 " --> pdb=" O ASP H 26 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG H 170 " --> pdb=" O TYR H 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 256 through 262 removed outlier: 3.846A pdb=" N PHE H 258 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 252 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS H 215 " --> pdb=" O ARG H 312 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 455 removed outlier: 6.837A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 463 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA7, first strand: chain 'H' and resid 513 through 514 Processing sheet with id=AA8, first strand: chain 'H' and resid 569 through 573 Processing sheet with id=AA9, first strand: chain 'H' and resid 589 through 591 removed outlier: 3.502A pdb=" N SER H 590 " --> pdb=" O CYS H 622 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS H 622 " --> pdb=" O SER H 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 628 through 631 removed outlier: 3.606A pdb=" N LYS H 640 " --> pdb=" O ILE H 629 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN H 638 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 650 through 651 removed outlier: 3.511A pdb=" N ASP H 651 " --> pdb=" O LEU H 654 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR H 664 " --> pdb=" O ASN H 659 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.422A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AB5, first strand: chain 'L' and resid 83 through 84 removed outlier: 3.696A pdb=" N THR L 89 " --> pdb=" O ASN L 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.464A pdb=" N ILE L 126 " --> pdb=" O ILE L 269 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE L 269 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.614A pdb=" N THR L 149 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 157 through 160 Processing sheet with id=AB9, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC1, first strand: chain 'L' and resid 207 through 212 177 hydrogen bonds defined for protein. 447 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: 1.24 Time building geometry restraints manager: 0.99 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: 2415 1.34 - 1.46: 1826 1.46 - 1.58: 3381 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 7707 Sorted by residual: bond pdb=" N ASP H 133 " pdb=" CA ASP H 133 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.65e+00 bond pdb=" N ILE H 134 " pdb=" CA ILE H 134 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.35e-02 5.49e+03 6.10e+00 bond pdb=" N SER H 131 " pdb=" CA SER H 131 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.04e+00 bond pdb=" N VAL H 132 " pdb=" CA VAL H 132 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.58e+00 bond pdb=" N ASN H 135 " pdb=" CA ASN H 135 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.46e-02 4.69e+03 3.97e+00 ... (remaining 7702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 10180 1.40 - 2.80: 192 2.80 - 4.20: 37 4.20 - 5.59: 16 5.59 - 6.99: 4 Bond angle restraints: 10429 Sorted by residual: angle pdb=" CA GLN L 51 " pdb=" CB GLN L 51 " pdb=" CG GLN L 51 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ASN H 135 " pdb=" C ASN H 135 " pdb=" O ASN H 135 " ideal model delta sigma weight residual 121.28 117.93 3.35 1.19e+00 7.06e-01 7.91e+00 angle pdb=" CB GLN L 51 " pdb=" CG GLN L 51 " pdb=" CD GLN L 51 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.70e+00 3.46e-01 7.49e+00 angle pdb=" CA ILE H 134 " pdb=" C ILE H 134 " pdb=" O ILE H 134 " ideal model delta sigma weight residual 120.22 117.91 2.31 8.90e-01 1.26e+00 6.73e+00 angle pdb=" CA ASP H 133 " pdb=" C ASP H 133 " pdb=" O ASP H 133 " ideal model delta sigma weight residual 121.16 118.36 2.80 1.13e+00 7.83e-01 6.16e+00 ... (remaining 10424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4253 17.99 - 35.98: 495 35.98 - 53.97: 125 53.97 - 71.96: 26 71.96 - 89.95: 16 Dihedral angle restraints: 4915 sinusoidal: 2190 harmonic: 2725 Sorted by residual: 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 -86.00 -175.95 89.95 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS H 412 " pdb=" SG CYS H 412 " pdb=" SG CYS H 425 " pdb=" CB CYS H 425 " ideal model delta sinusoidal sigma weight residual -86.00 -166.05 80.05 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS H 498 " pdb=" SG CYS H 498 " pdb=" SG CYS H 522 " pdb=" CB CYS H 522 " ideal model delta sinusoidal sigma weight residual -86.00 -164.22 78.22 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 4912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 872 0.044 - 0.089: 230 0.089 - 0.133: 63 0.133 - 0.177: 3 0.177 - 0.221: 2 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA VAL H 132 " pdb=" N VAL H 132 " pdb=" C VAL H 132 " pdb=" CB VAL H 132 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE H 134 " pdb=" N ILE H 134 " pdb=" C ILE H 134 " pdb=" CB ILE H 134 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN H 468 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 1167 not shown) Planarity restraints: 1333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 223 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO L 224 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 224 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 224 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 364 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO H 365 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 365 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 365 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 433 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO H 434 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO H 434 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 434 " 0.015 5.00e-02 4.00e+02 ... (remaining 1330 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 705 2.75 - 3.29: 7237 3.29 - 3.82: 11731 3.82 - 4.36: 13550 4.36 - 4.90: 24052 Nonbonded interactions: 57275 Sorted by model distance: nonbonded pdb=" OH TYR H 28 " pdb=" OE1 GLU H 417 " model vdw 2.212 3.040 nonbonded pdb=" O GLU L 203 " pdb=" OG SER L 206 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP H 26 " pdb=" OG1 THR L 73 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR L 92 " pdb=" OD2 ASP L 95 " model vdw 2.259 3.040 nonbonded pdb=" NE2 HIS H 63 " pdb=" OD1 ASP H 405 " model vdw 2.266 3.120 ... (remaining 57270 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.060 Find NCS groups from input model: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.002 0.035 7747 Z= 0.120 Angle : 0.544 9.133 10523 Z= 0.280 Chirality : 0.043 0.221 1170 Planarity : 0.003 0.039 1328 Dihedral : 16.464 87.201 3089 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.24 % Allowed : 23.61 % Favored : 76.14 % 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: -0.40 (0.28), residues: 914 helix: -0.08 (0.59), residues: 89 sheet: -0.32 (0.39), residues: 200 loop : -0.22 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 359 TYR 0.013 0.001 TYR L 122 PHE 0.016 0.001 PHE H 521 TRP 0.010 0.001 TRP L 200 HIS 0.004 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7707) covalent geometry : angle 0.52604 (10429) SS BOND : bond 0.00184 ( 26) SS BOND : angle 0.72907 ( 52) hydrogen bonds : bond 0.24559 ( 177) hydrogen bonds : angle 9.82709 ( 447) link_ALPHA1-2 : bond 0.00369 ( 2) link_ALPHA1-2 : angle 1.50725 ( 6) link_ALPHA1-3 : bond 0.00116 ( 1) link_ALPHA1-3 : angle 1.70840 ( 3) link_ALPHA1-6 : bond 0.00537 ( 1) link_ALPHA1-6 : angle 1.36764 ( 3) link_BETA1-4 : bond 0.00408 ( 5) link_BETA1-4 : angle 1.57347 ( 15) link_NAG-ASN : bond 0.00504 ( 5) link_NAG-ASN : angle 3.05009 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 257 TYR cc_start: 0.6903 (p90) cc_final: 0.6566 (p90) REVERT: L 242 TYR cc_start: 0.8401 (m-10) cc_final: 0.8107 (m-80) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.0880 time to fit residues: 11.3530 Evaluate side-chains 88 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 GLN H 576 ASN ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.204323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135008 restraints weight = 9029.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140535 restraints weight = 5457.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144210 restraints weight = 4099.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146165 restraints weight = 3467.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147617 restraints weight = 3158.713| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7747 Z= 0.178 Angle : 0.587 10.765 10523 Z= 0.297 Chirality : 0.046 0.190 1170 Planarity : 0.003 0.038 1328 Dihedral : 7.872 66.855 1299 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.25 % Allowed : 20.84 % Favored : 75.90 % 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: -0.42 (0.28), residues: 914 helix: -0.02 (0.57), residues: 95 sheet: -0.53 (0.38), residues: 196 loop : -0.17 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 359 TYR 0.019 0.001 TYR H 27 PHE 0.018 0.002 PHE H 173 TRP 0.008 0.001 TRP L 223 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7707) covalent geometry : angle 0.55843 (10429) SS BOND : bond 0.00277 ( 26) SS BOND : angle 1.09505 ( 52) hydrogen bonds : bond 0.03890 ( 177) hydrogen bonds : angle 6.89968 ( 447) link_ALPHA1-2 : bond 0.00304 ( 2) link_ALPHA1-2 : angle 1.43777 ( 6) link_ALPHA1-3 : bond 0.00292 ( 1) link_ALPHA1-3 : angle 1.70272 ( 3) link_ALPHA1-6 : bond 0.00693 ( 1) link_ALPHA1-6 : angle 1.44823 ( 3) link_BETA1-4 : bond 0.00354 ( 5) link_BETA1-4 : angle 2.28358 ( 15) link_NAG-ASN : bond 0.00514 ( 5) link_NAG-ASN : angle 3.69617 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 224 ASP cc_start: 0.6556 (t0) cc_final: 0.6301 (t0) REVERT: H 475 VAL cc_start: 0.6528 (OUTLIER) cc_final: 0.6203 (p) REVERT: H 541 GLU cc_start: 0.8384 (pm20) cc_final: 0.7811 (pm20) REVERT: L 51 GLN cc_start: 0.8781 (pp30) cc_final: 0.8528 (pp30) REVERT: L 107 MET cc_start: 0.8492 (mmt) cc_final: 0.8208 (mmt) outliers start: 27 outliers final: 14 residues processed: 112 average time/residue: 0.0790 time to fit residues: 12.6935 Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 85 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 ASN H 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135609 restraints weight = 9020.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141328 restraints weight = 5379.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145058 restraints weight = 4040.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146982 restraints weight = 3414.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148544 restraints weight = 3119.216| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7747 Z= 0.141 Angle : 0.562 11.237 10523 Z= 0.281 Chirality : 0.045 0.188 1170 Planarity : 0.003 0.039 1328 Dihedral : 7.425 62.568 1299 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.98 % Allowed : 20.12 % Favored : 75.90 % 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: -0.47 (0.28), residues: 914 helix: -0.07 (0.56), residues: 95 sheet: -0.50 (0.39), residues: 194 loop : -0.22 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 359 TYR 0.014 0.001 TYR H 166 PHE 0.013 0.001 PHE H 53 TRP 0.009 0.001 TRP L 200 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7707) covalent geometry : angle 0.53395 (10429) SS BOND : bond 0.00274 ( 26) SS BOND : angle 0.91391 ( 52) hydrogen bonds : bond 0.03435 ( 177) hydrogen bonds : angle 6.51758 ( 447) link_ALPHA1-2 : bond 0.00341 ( 2) link_ALPHA1-2 : angle 1.53851 ( 6) link_ALPHA1-3 : bond 0.00448 ( 1) link_ALPHA1-3 : angle 1.75220 ( 3) link_ALPHA1-6 : bond 0.00763 ( 1) link_ALPHA1-6 : angle 1.38101 ( 3) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 2.07283 ( 15) link_NAG-ASN : bond 0.00580 ( 5) link_NAG-ASN : angle 3.81495 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 224 ASP cc_start: 0.6548 (t0) cc_final: 0.6282 (t0) REVERT: H 485 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5943 (p0) REVERT: L 51 GLN cc_start: 0.8870 (pp30) cc_final: 0.8459 (pp30) REVERT: L 196 TYR cc_start: 0.8008 (m-80) cc_final: 0.7781 (m-80) outliers start: 33 outliers final: 18 residues processed: 117 average time/residue: 0.0833 time to fit residues: 13.8358 Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 ASN H 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135622 restraints weight = 9153.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141392 restraints weight = 5422.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145044 restraints weight = 4042.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147365 restraints weight = 3419.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148590 restraints weight = 3101.276| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7747 Z= 0.132 Angle : 0.580 11.498 10523 Z= 0.289 Chirality : 0.044 0.182 1170 Planarity : 0.003 0.040 1328 Dihedral : 7.109 57.274 1299 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.22 % Allowed : 21.45 % Favored : 74.34 % 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: -0.49 (0.28), residues: 914 helix: -0.05 (0.56), residues: 95 sheet: -0.33 (0.39), residues: 193 loop : -0.32 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 359 TYR 0.014 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.010 0.001 TRP L 200 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7707) covalent geometry : angle 0.54769 (10429) SS BOND : bond 0.00274 ( 26) SS BOND : angle 1.29606 ( 52) hydrogen bonds : bond 0.03085 ( 177) hydrogen bonds : angle 6.26311 ( 447) link_ALPHA1-2 : bond 0.00328 ( 2) link_ALPHA1-2 : angle 1.57118 ( 6) link_ALPHA1-3 : bond 0.00512 ( 1) link_ALPHA1-3 : angle 1.74935 ( 3) link_ALPHA1-6 : bond 0.00807 ( 1) link_ALPHA1-6 : angle 1.35382 ( 3) link_BETA1-4 : bond 0.00411 ( 5) link_BETA1-4 : angle 2.03682 ( 15) link_NAG-ASN : bond 0.00593 ( 5) link_NAG-ASN : angle 3.88904 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 224 ASP cc_start: 0.6677 (t0) cc_final: 0.6411 (t0) REVERT: H 320 ASP cc_start: 0.7888 (p0) cc_final: 0.7468 (p0) REVERT: H 485 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.5953 (p0) REVERT: H 511 TRP cc_start: 0.8125 (m100) cc_final: 0.7114 (m100) REVERT: H 541 GLU cc_start: 0.8036 (pm20) cc_final: 0.7457 (pm20) REVERT: L 51 GLN cc_start: 0.8899 (pp30) cc_final: 0.8417 (pp30) outliers start: 35 outliers final: 20 residues processed: 119 average time/residue: 0.0728 time to fit residues: 12.4878 Evaluate side-chains 108 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 21 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 ASN H 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.203692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134785 restraints weight = 9035.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140441 restraints weight = 5390.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144267 restraints weight = 4029.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146322 restraints weight = 3399.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147881 restraints weight = 3087.781| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7747 Z= 0.145 Angle : 0.578 11.664 10523 Z= 0.288 Chirality : 0.045 0.188 1170 Planarity : 0.003 0.040 1328 Dihedral : 6.875 53.461 1299 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.98 % Allowed : 21.20 % Favored : 74.82 % 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: 914 helix: -0.10 (0.56), residues: 95 sheet: -0.35 (0.39), residues: 195 loop : -0.31 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 118 TYR 0.015 0.001 TYR H 27 PHE 0.013 0.002 PHE H 521 TRP 0.011 0.001 TRP L 200 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7707) covalent geometry : angle 0.54809 (10429) SS BOND : bond 0.00303 ( 26) SS BOND : angle 1.08926 ( 52) hydrogen bonds : bond 0.03023 ( 177) hydrogen bonds : angle 6.19777 ( 447) link_ALPHA1-2 : bond 0.00329 ( 2) link_ALPHA1-2 : angle 1.57991 ( 6) link_ALPHA1-3 : bond 0.00532 ( 1) link_ALPHA1-3 : angle 1.83986 ( 3) link_ALPHA1-6 : bond 0.00838 ( 1) link_ALPHA1-6 : angle 1.36379 ( 3) link_BETA1-4 : bond 0.00418 ( 5) link_BETA1-4 : angle 2.01691 ( 15) link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 3.92754 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (mmmt) REVERT: H 320 ASP cc_start: 0.7875 (p0) cc_final: 0.7460 (p0) REVERT: H 485 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5879 (p0) REVERT: H 511 TRP cc_start: 0.8151 (m100) cc_final: 0.6847 (m100) REVERT: H 531 MET cc_start: 0.7960 (tmm) cc_final: 0.7437 (tmm) REVERT: H 541 GLU cc_start: 0.8108 (pm20) cc_final: 0.7638 (pm20) REVERT: L 51 GLN cc_start: 0.8967 (pp30) cc_final: 0.8455 (pp30) REVERT: L 196 TYR cc_start: 0.7990 (m-80) cc_final: 0.7644 (m-80) outliers start: 33 outliers final: 23 residues processed: 114 average time/residue: 0.0782 time to fit residues: 12.6047 Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.202331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132700 restraints weight = 9094.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138455 restraints weight = 5413.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141888 restraints weight = 4040.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144340 restraints weight = 3423.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145417 restraints weight = 3094.044| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7747 Z= 0.181 Angle : 0.598 11.839 10523 Z= 0.299 Chirality : 0.046 0.190 1170 Planarity : 0.003 0.041 1328 Dihedral : 6.874 52.627 1299 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.46 % Allowed : 20.48 % Favored : 75.06 % 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: -0.57 (0.28), residues: 914 helix: -0.17 (0.56), residues: 95 sheet: -0.43 (0.39), residues: 195 loop : -0.34 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 118 TYR 0.017 0.001 TYR H 27 PHE 0.015 0.002 PHE H 53 TRP 0.013 0.002 TRP L 200 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7707) covalent geometry : angle 0.56753 (10429) SS BOND : bond 0.00330 ( 26) SS BOND : angle 1.18975 ( 52) hydrogen bonds : bond 0.03160 ( 177) hydrogen bonds : angle 6.22719 ( 447) link_ALPHA1-2 : bond 0.00306 ( 2) link_ALPHA1-2 : angle 1.56031 ( 6) link_ALPHA1-3 : bond 0.00433 ( 1) link_ALPHA1-3 : angle 1.98590 ( 3) link_ALPHA1-6 : bond 0.00907 ( 1) link_ALPHA1-6 : angle 1.39657 ( 3) link_BETA1-4 : bond 0.00370 ( 5) link_BETA1-4 : angle 2.09319 ( 15) link_NAG-ASN : bond 0.00579 ( 5) link_NAG-ASN : angle 3.96835 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7380 (mmmt) REVERT: H 224 ASP cc_start: 0.6626 (t0) cc_final: 0.6399 (t0) REVERT: H 320 ASP cc_start: 0.7907 (p0) cc_final: 0.7544 (p0) REVERT: H 481 TYR cc_start: 0.7972 (p90) cc_final: 0.6987 (p90) REVERT: H 485 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5895 (p0) REVERT: H 511 TRP cc_start: 0.8136 (m100) cc_final: 0.6829 (m100) REVERT: H 541 GLU cc_start: 0.8121 (pm20) cc_final: 0.7686 (pm20) REVERT: L 51 GLN cc_start: 0.9024 (pp30) cc_final: 0.8440 (pp30) REVERT: L 196 TYR cc_start: 0.8087 (m-80) cc_final: 0.7819 (m-80) outliers start: 37 outliers final: 27 residues processed: 117 average time/residue: 0.0829 time to fit residues: 13.6888 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 360 LEU Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 269 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 82 optimal weight: 0.0980 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.202450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132853 restraints weight = 9048.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138525 restraints weight = 5370.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142278 restraints weight = 4014.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144206 restraints weight = 3385.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145537 restraints weight = 3083.039| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7747 Z= 0.172 Angle : 0.602 11.900 10523 Z= 0.301 Chirality : 0.046 0.187 1170 Planarity : 0.003 0.041 1328 Dihedral : 6.800 51.237 1299 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.46 % Allowed : 20.72 % Favored : 74.82 % 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: 914 helix: -0.17 (0.56), residues: 95 sheet: -0.30 (0.40), residues: 185 loop : -0.41 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 118 TYR 0.018 0.001 TYR H 481 PHE 0.015 0.002 PHE H 521 TRP 0.013 0.002 TRP L 200 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7707) covalent geometry : angle 0.57146 (10429) SS BOND : bond 0.00308 ( 26) SS BOND : angle 1.11816 ( 52) hydrogen bonds : bond 0.03239 ( 177) hydrogen bonds : angle 6.22636 ( 447) link_ALPHA1-2 : bond 0.00376 ( 2) link_ALPHA1-2 : angle 1.61014 ( 6) link_ALPHA1-3 : bond 0.00422 ( 1) link_ALPHA1-3 : angle 1.96061 ( 3) link_ALPHA1-6 : bond 0.00976 ( 1) link_ALPHA1-6 : angle 1.38780 ( 3) link_BETA1-4 : bond 0.00357 ( 5) link_BETA1-4 : angle 2.06205 ( 15) link_NAG-ASN : bond 0.00594 ( 5) link_NAG-ASN : angle 3.99988 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7464 (mmmt) REVERT: H 224 ASP cc_start: 0.6652 (t0) cc_final: 0.6407 (t0) REVERT: H 320 ASP cc_start: 0.7861 (p0) cc_final: 0.7484 (p0) REVERT: H 481 TYR cc_start: 0.8060 (p90) cc_final: 0.7398 (p90) REVERT: H 485 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5890 (p0) REVERT: H 495 LYS cc_start: 0.7571 (ptmm) cc_final: 0.7203 (ptmt) REVERT: H 511 TRP cc_start: 0.8187 (m100) cc_final: 0.6901 (m100) REVERT: H 541 GLU cc_start: 0.8147 (pm20) cc_final: 0.7774 (pm20) REVERT: L 51 GLN cc_start: 0.9050 (pp30) cc_final: 0.8448 (pp30) REVERT: L 196 TYR cc_start: 0.8161 (m-80) cc_final: 0.7939 (m-80) outliers start: 37 outliers final: 27 residues processed: 117 average time/residue: 0.0931 time to fit residues: 14.8320 Evaluate side-chains 119 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 379 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 157 VAL Chi-restraints excluded: chain L residue 173 TRP Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain L residue 277 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 HIS H 576 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.198375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130554 restraints weight = 9080.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.135666 restraints weight = 5568.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139082 restraints weight = 4211.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140947 restraints weight = 3591.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142003 restraints weight = 3277.291| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7747 Z= 0.122 Angle : 0.581 11.735 10523 Z= 0.289 Chirality : 0.045 0.178 1170 Planarity : 0.003 0.041 1328 Dihedral : 6.470 51.284 1299 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.49 % Allowed : 21.20 % Favored : 75.30 % 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: -0.67 (0.28), residues: 914 helix: -0.13 (0.57), residues: 95 sheet: -0.38 (0.37), residues: 214 loop : -0.48 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 273 TYR 0.014 0.001 TYR H 27 PHE 0.020 0.001 PHE H 521 TRP 0.013 0.001 TRP L 200 HIS 0.002 0.001 HIS H 368 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7707) covalent geometry : angle 0.55148 (10429) SS BOND : bond 0.00239 ( 26) SS BOND : angle 0.98674 ( 52) hydrogen bonds : bond 0.02940 ( 177) hydrogen bonds : angle 6.10058 ( 447) link_ALPHA1-2 : bond 0.00384 ( 2) link_ALPHA1-2 : angle 1.65294 ( 6) link_ALPHA1-3 : bond 0.00645 ( 1) link_ALPHA1-3 : angle 1.90804 ( 3) link_ALPHA1-6 : bond 0.00874 ( 1) link_ALPHA1-6 : angle 1.36442 ( 3) link_BETA1-4 : bond 0.00443 ( 5) link_BETA1-4 : angle 1.95344 ( 15) link_NAG-ASN : bond 0.00617 ( 5) link_NAG-ASN : angle 3.97392 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 224 ASP cc_start: 0.6678 (t0) cc_final: 0.6467 (t0) REVERT: H 320 ASP cc_start: 0.7894 (p0) cc_final: 0.7694 (p0) REVERT: H 485 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.5828 (p0) REVERT: H 511 TRP cc_start: 0.8097 (m100) cc_final: 0.6682 (m100) REVERT: H 541 GLU cc_start: 0.8134 (pm20) cc_final: 0.7781 (pm20) REVERT: L 51 GLN cc_start: 0.9010 (pp30) cc_final: 0.8360 (pp30) outliers start: 29 outliers final: 21 residues processed: 111 average time/residue: 0.0751 time to fit residues: 11.8167 Evaluate side-chains 110 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 477 CYS Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain H residue 579 MET Chi-restraints excluded: chain L residue 31 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 173 TRP Chi-restraints excluded: chain L residue 277 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.201110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137727 restraints weight = 9112.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138409 restraints weight = 5365.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139548 restraints weight = 4602.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141038 restraints weight = 4314.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140991 restraints weight = 3751.213| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7747 Z= 0.206 Angle : 0.631 11.975 10523 Z= 0.318 Chirality : 0.047 0.192 1170 Planarity : 0.004 0.041 1328 Dihedral : 6.710 50.846 1299 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.37 % Allowed : 21.08 % Favored : 75.54 % 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: -0.73 (0.27), residues: 914 helix: -0.32 (0.55), residues: 95 sheet: -0.43 (0.39), residues: 187 loop : -0.50 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 118 TYR 0.018 0.002 TYR H 27 PHE 0.017 0.002 PHE H 521 TRP 0.017 0.002 TRP H 435 HIS 0.003 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 7707) covalent geometry : angle 0.60114 (10429) SS BOND : bond 0.00331 ( 26) SS BOND : angle 1.21232 ( 52) hydrogen bonds : bond 0.03376 ( 177) hydrogen bonds : angle 6.32798 ( 447) link_ALPHA1-2 : bond 0.00303 ( 2) link_ALPHA1-2 : angle 1.60595 ( 6) link_ALPHA1-3 : bond 0.00337 ( 1) link_ALPHA1-3 : angle 2.16190 ( 3) link_ALPHA1-6 : bond 0.00984 ( 1) link_ALPHA1-6 : angle 1.41921 ( 3) link_BETA1-4 : bond 0.00326 ( 5) link_BETA1-4 : angle 2.14588 ( 15) link_NAG-ASN : bond 0.00592 ( 5) link_NAG-ASN : angle 3.98383 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7499 (mmmt) REVERT: H 224 ASP cc_start: 0.6912 (t0) cc_final: 0.6618 (t0) REVERT: H 320 ASP cc_start: 0.7928 (p0) cc_final: 0.7602 (p0) REVERT: H 485 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5667 (p0) REVERT: H 511 TRP cc_start: 0.8083 (m100) cc_final: 0.6717 (m100) REVERT: H 541 GLU cc_start: 0.8136 (pm20) cc_final: 0.7569 (pm20) REVERT: H 553 ARG cc_start: 0.8243 (ptt90) cc_final: 0.7665 (ptt90) REVERT: L 51 GLN cc_start: 0.9052 (pp30) cc_final: 0.8401 (pp30) REVERT: L 196 TYR cc_start: 0.8166 (m-80) cc_final: 0.7785 (m-80) outliers start: 28 outliers final: 20 residues processed: 112 average time/residue: 0.0880 time to fit residues: 13.6848 Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 173 TRP Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 576 ASN L 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.196087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132018 restraints weight = 8964.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134142 restraints weight = 5876.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136247 restraints weight = 4658.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137236 restraints weight = 4010.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137508 restraints weight = 3872.254| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 0.032 7747 Z= 0.116 Angle : 0.590 11.629 10523 Z= 0.295 Chirality : 0.045 0.232 1170 Planarity : 0.003 0.042 1328 Dihedral : 6.310 51.413 1299 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.65 % Allowed : 22.05 % Favored : 75.30 % 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: -0.69 (0.28), residues: 914 helix: -0.12 (0.56), residues: 95 sheet: -0.51 (0.37), residues: 217 loop : -0.45 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 118 TYR 0.015 0.001 TYR H 50 PHE 0.023 0.001 PHE H 521 TRP 0.010 0.001 TRP L 200 HIS 0.002 0.001 HIS H 368 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7707) covalent geometry : angle 0.56195 (10429) SS BOND : bond 0.00227 ( 26) SS BOND : angle 0.96664 ( 52) hydrogen bonds : bond 0.02945 ( 177) hydrogen bonds : angle 6.07535 ( 447) link_ALPHA1-2 : bond 0.00432 ( 2) link_ALPHA1-2 : angle 1.66595 ( 6) link_ALPHA1-3 : bond 0.00787 ( 1) link_ALPHA1-3 : angle 1.90684 ( 3) link_ALPHA1-6 : bond 0.00866 ( 1) link_ALPHA1-6 : angle 1.35203 ( 3) link_BETA1-4 : bond 0.00472 ( 5) link_BETA1-4 : angle 1.91516 ( 15) link_NAG-ASN : bond 0.00619 ( 5) link_NAG-ASN : angle 3.95869 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7448 (mmmt) REVERT: H 224 ASP cc_start: 0.6715 (t0) cc_final: 0.6438 (t0) REVERT: H 485 ASP cc_start: 0.6287 (OUTLIER) cc_final: 0.5652 (p0) REVERT: H 511 TRP cc_start: 0.8044 (m100) cc_final: 0.6605 (m100) REVERT: H 541 GLU cc_start: 0.8126 (pm20) cc_final: 0.7817 (pm20) REVERT: L 51 GLN cc_start: 0.9011 (pp30) cc_final: 0.8313 (pp30) REVERT: L 136 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7418 (mm-30) REVERT: L 196 TYR cc_start: 0.8100 (m-80) cc_final: 0.7667 (m-80) REVERT: L 265 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7615 (mmmt) outliers start: 22 outliers final: 17 residues processed: 105 average time/residue: 0.0821 time to fit residues: 12.2536 Evaluate side-chains 107 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 214 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 414 MET Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 475 VAL Chi-restraints excluded: chain H residue 485 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain L residue 173 TRP Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 277 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 56 optimal weight: 20.0000 chunk 64 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.200370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138141 restraints weight = 8994.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138187 restraints weight = 5587.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142782 restraints weight = 4323.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143840 restraints weight = 3591.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144095 restraints weight = 3299.499| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7747 Z= 0.100 Angle : 0.573 11.365 10523 Z= 0.284 Chirality : 0.044 0.212 1170 Planarity : 0.003 0.042 1328 Dihedral : 5.745 51.063 1299 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.41 % Allowed : 22.17 % Favored : 75.42 % 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: -0.53 (0.28), residues: 914 helix: -0.09 (0.57), residues: 95 sheet: -0.19 (0.39), residues: 194 loop : -0.41 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 118 TYR 0.013 0.001 TYR H 27 PHE 0.023 0.001 PHE H 521 TRP 0.008 0.001 TRP L 200 HIS 0.005 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 7707) covalent geometry : angle 0.54597 (10429) SS BOND : bond 0.00228 ( 26) SS BOND : angle 0.93730 ( 52) hydrogen bonds : bond 0.02796 ( 177) hydrogen bonds : angle 5.88816 ( 447) link_ALPHA1-2 : bond 0.00431 ( 2) link_ALPHA1-2 : angle 1.60734 ( 6) link_ALPHA1-3 : bond 0.00927 ( 1) link_ALPHA1-3 : angle 1.76900 ( 3) link_ALPHA1-6 : bond 0.00707 ( 1) link_ALPHA1-6 : angle 1.40709 ( 3) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.84060 ( 15) link_NAG-ASN : bond 0.00633 ( 5) link_NAG-ASN : angle 3.80923 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1454.24 seconds wall clock time: 25 minutes 49.07 seconds (1549.07 seconds total)