Starting phenix.real_space_refine on Wed Mar 4 00:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujc_20796/03_2026/6ujc_20796.map" } resolution = 3.56 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= 0.048 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 43 5.16 5 C 5803 2.51 5 N 1553 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 9209 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4387 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'ARG:plan': 5, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9209 At special positions: 0 Unit cell: (72.63, 100.875, 164.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 43 16.00 Mg 1 11.99 O 1804 8.00 N 1553 7.00 C 5803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.16 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.04 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 98 " distance=2.04 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 C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG G 1 " - " ASN B 191 " " NAG H 1 " - " ASN B 389 " " NAG I 1 " - " ASN B 414 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 313.7 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.3% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 123 through 126 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.810A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.032A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.852A pdb=" N LEU F 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.034A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.010A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.537A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.498A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 5.665A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.746A pdb=" N LEU A 454 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.554A pdb=" N CYS A 461 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.654A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.330A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.453A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.808A pdb=" N LEU F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR F 59 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 45 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 344 hydrogen bonds defined for protein. 873 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: 1.68 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1936 1.32 - 1.45: 2441 1.45 - 1.58: 4947 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 9395 Sorted by residual: bond pdb=" NE ARG F 32 " pdb=" CZ ARG F 32 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.21e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 10563 1.71 - 3.42: 1768 3.42 - 5.13: 314 5.13 - 6.84: 85 6.84 - 8.54: 14 Bond angle restraints: 12744 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.10 -8.54 1.02e+00 9.61e-01 7.02e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.02 -8.46 1.02e+00 9.61e-01 6.88e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.27e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.45 -7.89 1.02e+00 9.61e-01 5.98e+01 angle pdb=" C LEU A 463 " pdb=" N PRO A 464 " pdb=" CA PRO A 464 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 ... (remaining 12739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 5669 21.51 - 43.01: 107 43.01 - 64.52: 30 64.52 - 86.02: 19 86.02 - 107.53: 7 Dihedral angle restraints: 5832 sinusoidal: 2437 harmonic: 3395 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 41.37 51.63 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.19 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 5829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 998 0.074 - 0.148: 342 0.148 - 0.221: 74 0.221 - 0.295: 27 0.295 - 0.369: 15 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.90e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 MAN C 6 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 6 " pdb=" O5 MAN C 6 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 ... (remaining 1453 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.09e-02 1.19e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.027 2.00e-02 2.50e+03 2.82e-02 9.93e+00 pdb=" CG ASN A 44 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " 0.030 2.00e-02 2.50e+03 1.54e-02 4.75e+00 pdb=" CG TYR B 103 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " 0.018 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 30 2.41 - 3.04: 5613 3.04 - 3.66: 12870 3.66 - 4.28: 21662 4.28 - 4.90: 34679 Nonbonded interactions: 74854 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.792 2.170 nonbonded pdb=" OD1 ASP F 34 " pdb="MG MG B2002 " model vdw 1.885 2.170 nonbonded pdb=" OD2 ASP F 34 " pdb="MG MG B2002 " model vdw 1.901 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.003 2.170 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.081 2.510 ... (remaining 74849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.014 0.129 9421 Z= 0.760 Angle : 1.406 8.544 12813 Z= 0.948 Chirality : 0.087 0.369 1456 Planarity : 0.006 0.028 1648 Dihedral : 11.400 107.525 3635 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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 (0.23), residues: 1174 helix: -1.21 (0.44), residues: 95 sheet: 0.80 (0.23), residues: 457 loop : 0.32 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 32 TYR 0.030 0.005 TYR B 103 PHE 0.024 0.004 PHE A 276 TRP 0.020 0.006 TRP B 308 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.01379 ( 9395) covalent geometry : angle 1.39568 (12744) SS BOND : bond 0.04336 ( 9) SS BOND : angle 2.07281 ( 18) hydrogen bonds : bond 0.16567 ( 332) hydrogen bonds : angle 9.04010 ( 873) link_ALPHA1-2 : bond 0.07253 ( 1) link_ALPHA1-2 : angle 3.58567 ( 3) link_ALPHA1-3 : bond 0.07330 ( 1) link_ALPHA1-3 : angle 3.45177 ( 3) link_ALPHA1-6 : bond 0.05101 ( 1) link_ALPHA1-6 : angle 2.69440 ( 3) link_BETA1-4 : bond 0.06247 ( 6) link_BETA1-4 : angle 3.52250 ( 18) link_NAG-ASN : bond 0.06459 ( 8) link_NAG-ASN : angle 2.15531 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7852 (ptm) cc_final: 0.7498 (ptp) REVERT: E 52 ASN cc_start: 0.7606 (t0) cc_final: 0.6974 (p0) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1145 time to fit residues: 24.5116 Evaluate side-chains 70 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 100 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105424 restraints weight = 20875.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108379 restraints weight = 11193.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110346 restraints weight = 7139.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111673 restraints weight = 5159.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112548 restraints weight = 4037.155| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9421 Z= 0.162 Angle : 0.678 14.197 12813 Z= 0.344 Chirality : 0.048 0.184 1456 Planarity : 0.004 0.054 1648 Dihedral : 7.645 87.218 1620 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.83 % Allowed : 6.23 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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 (0.24), residues: 1174 helix: 0.05 (0.54), residues: 90 sheet: 0.80 (0.22), residues: 465 loop : 0.15 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 476 TYR 0.015 0.002 TYR A 265 PHE 0.016 0.001 PHE A 276 TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9395) covalent geometry : angle 0.65647 (12744) SS BOND : bond 0.01081 ( 9) SS BOND : angle 2.18570 ( 18) hydrogen bonds : bond 0.04141 ( 332) hydrogen bonds : angle 7.04988 ( 873) link_ALPHA1-2 : bond 0.00569 ( 1) link_ALPHA1-2 : angle 1.60658 ( 3) link_ALPHA1-3 : bond 0.01444 ( 1) link_ALPHA1-3 : angle 1.28908 ( 3) link_ALPHA1-6 : bond 0.00852 ( 1) link_ALPHA1-6 : angle 1.48170 ( 3) link_BETA1-4 : bond 0.01301 ( 6) link_BETA1-4 : angle 3.23474 ( 18) link_NAG-ASN : bond 0.00354 ( 8) link_NAG-ASN : angle 2.01979 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8135 (ptm) cc_final: 0.7768 (ptp) REVERT: B 117 MET cc_start: 0.8492 (mmm) cc_final: 0.8197 (tpp) REVERT: B 392 VAL cc_start: 0.8688 (t) cc_final: 0.8456 (p) REVERT: E 52 ASN cc_start: 0.7410 (t0) cc_final: 0.6085 (p0) REVERT: F 100 GLN cc_start: 0.8521 (pp30) cc_final: 0.8302 (pp30) outliers start: 17 outliers final: 9 residues processed: 94 average time/residue: 0.1027 time to fit residues: 13.3567 Evaluate side-chains 66 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.120763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102535 restraints weight = 20984.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105420 restraints weight = 11484.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107385 restraints weight = 7506.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108697 restraints weight = 5452.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109614 restraints weight = 4311.801| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9421 Z= 0.150 Angle : 0.611 13.011 12813 Z= 0.308 Chirality : 0.046 0.204 1456 Planarity : 0.004 0.029 1648 Dihedral : 6.404 67.544 1620 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.61 % Allowed : 7.20 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1174 helix: 0.33 (0.56), residues: 89 sheet: 0.72 (0.23), residues: 452 loop : 0.06 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 164 TYR 0.027 0.001 TYR A 265 PHE 0.015 0.001 PHE A 477 TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9395) covalent geometry : angle 0.59699 (12744) SS BOND : bond 0.00249 ( 9) SS BOND : angle 1.19792 ( 18) hydrogen bonds : bond 0.03588 ( 332) hydrogen bonds : angle 6.41083 ( 873) link_ALPHA1-2 : bond 0.00654 ( 1) link_ALPHA1-2 : angle 1.31086 ( 3) link_ALPHA1-3 : bond 0.01200 ( 1) link_ALPHA1-3 : angle 1.47065 ( 3) link_ALPHA1-6 : bond 0.01152 ( 1) link_ALPHA1-6 : angle 1.39211 ( 3) link_BETA1-4 : bond 0.01252 ( 6) link_BETA1-4 : angle 2.64038 ( 18) link_NAG-ASN : bond 0.00420 ( 8) link_NAG-ASN : angle 1.77482 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8225 (ptm) cc_final: 0.7872 (ptp) REVERT: B 117 MET cc_start: 0.8421 (mmm) cc_final: 0.8214 (tpp) REVERT: B 392 VAL cc_start: 0.8682 (t) cc_final: 0.8428 (p) REVERT: E 52 ASN cc_start: 0.7541 (t0) cc_final: 0.6928 (t0) REVERT: E 111 THR cc_start: 0.7797 (m) cc_final: 0.7591 (p) REVERT: F 21 MET cc_start: 0.7571 (ptp) cc_final: 0.7102 (ptp) REVERT: F 87 SER cc_start: 0.6258 (m) cc_final: 0.5565 (t) REVERT: F 100 GLN cc_start: 0.8613 (pp30) cc_final: 0.8357 (pp30) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.0888 time to fit residues: 9.3470 Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.0010 chunk 61 optimal weight: 0.0770 chunk 103 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102820 restraints weight = 21524.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105594 restraints weight = 11973.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107513 restraints weight = 7872.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108803 restraints weight = 5746.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109639 restraints weight = 4539.767| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9421 Z= 0.114 Angle : 0.546 12.637 12813 Z= 0.273 Chirality : 0.046 0.254 1456 Planarity : 0.004 0.029 1648 Dihedral : 5.746 58.468 1620 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.72 % Allowed : 7.84 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.54 (0.24), residues: 1174 helix: 0.53 (0.58), residues: 90 sheet: 0.83 (0.24), residues: 454 loop : 0.06 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 86 TYR 0.015 0.001 TYR A 265 PHE 0.010 0.001 PHE A 276 TRP 0.010 0.001 TRP E 47 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9395) covalent geometry : angle 0.53211 (12744) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.80273 ( 18) hydrogen bonds : bond 0.03061 ( 332) hydrogen bonds : angle 6.07996 ( 873) link_ALPHA1-2 : bond 0.00506 ( 1) link_ALPHA1-2 : angle 1.52216 ( 3) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 1.89818 ( 3) link_ALPHA1-6 : bond 0.01081 ( 1) link_ALPHA1-6 : angle 1.47567 ( 3) link_BETA1-4 : bond 0.01173 ( 6) link_BETA1-4 : angle 2.57429 ( 18) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 1.61371 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6493 (ptp) REVERT: A 400 MET cc_start: 0.8280 (ptm) cc_final: 0.7972 (ptp) REVERT: B 94 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7050 (ppp) REVERT: B 117 MET cc_start: 0.8419 (mmm) cc_final: 0.8206 (tpp) REVERT: E 111 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7747 (p) outliers start: 16 outliers final: 9 residues processed: 70 average time/residue: 0.0913 time to fit residues: 9.3196 Evaluate side-chains 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102083 restraints weight = 20943.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104951 restraints weight = 11538.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106925 restraints weight = 7575.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108218 restraints weight = 5559.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109148 restraints weight = 4430.390| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9421 Z= 0.128 Angle : 0.553 12.116 12813 Z= 0.275 Chirality : 0.045 0.256 1456 Planarity : 0.003 0.030 1648 Dihedral : 5.463 52.598 1620 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.40 % Allowed : 8.59 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: 0.48 (0.25), residues: 1174 helix: 0.58 (0.58), residues: 90 sheet: 0.80 (0.24), residues: 454 loop : 0.01 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.011 0.001 TYR A 112 PHE 0.012 0.001 PHE A 477 TRP 0.010 0.001 TRP E 47 HIS 0.002 0.000 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9395) covalent geometry : angle 0.54013 (12744) SS BOND : bond 0.00239 ( 9) SS BOND : angle 0.62643 ( 18) hydrogen bonds : bond 0.03107 ( 332) hydrogen bonds : angle 5.98363 ( 873) link_ALPHA1-2 : bond 0.00516 ( 1) link_ALPHA1-2 : angle 1.49602 ( 3) link_ALPHA1-3 : bond 0.01118 ( 1) link_ALPHA1-3 : angle 1.93485 ( 3) link_ALPHA1-6 : bond 0.01045 ( 1) link_ALPHA1-6 : angle 1.42833 ( 3) link_BETA1-4 : bond 0.01103 ( 6) link_BETA1-4 : angle 2.48325 ( 18) link_NAG-ASN : bond 0.00249 ( 8) link_NAG-ASN : angle 1.59295 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7711 (mtp) cc_final: 0.7359 (mtp) REVERT: A 400 MET cc_start: 0.8273 (ptm) cc_final: 0.7986 (ptp) REVERT: B 94 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7350 (ppp) REVERT: B 117 MET cc_start: 0.8439 (mmm) cc_final: 0.8229 (tpp) REVERT: B 177 MET cc_start: 0.7995 (ttp) cc_final: 0.7765 (ttp) REVERT: E 111 THR cc_start: 0.7962 (m) cc_final: 0.7752 (p) REVERT: F 87 SER cc_start: 0.6194 (m) cc_final: 0.5796 (t) outliers start: 13 outliers final: 11 residues processed: 64 average time/residue: 0.0938 time to fit residues: 8.5636 Evaluate side-chains 61 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101238 restraints weight = 21119.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104082 restraints weight = 11667.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106016 restraints weight = 7684.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107298 restraints weight = 5655.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108203 restraints weight = 4510.955| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9421 Z= 0.134 Angle : 0.552 11.366 12813 Z= 0.276 Chirality : 0.045 0.252 1456 Planarity : 0.003 0.031 1648 Dihedral : 5.255 48.046 1620 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.83 % Allowed : 8.59 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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 (0.25), residues: 1174 helix: 0.64 (0.58), residues: 90 sheet: 0.72 (0.24), residues: 460 loop : -0.05 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.012 0.001 TYR A 112 PHE 0.013 0.001 PHE A 477 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9395) covalent geometry : angle 0.53902 (12744) SS BOND : bond 0.00209 ( 9) SS BOND : angle 0.62892 ( 18) hydrogen bonds : bond 0.03038 ( 332) hydrogen bonds : angle 5.85613 ( 873) link_ALPHA1-2 : bond 0.00522 ( 1) link_ALPHA1-2 : angle 1.56170 ( 3) link_ALPHA1-3 : bond 0.01145 ( 1) link_ALPHA1-3 : angle 1.96813 ( 3) link_ALPHA1-6 : bond 0.01057 ( 1) link_ALPHA1-6 : angle 1.37931 ( 3) link_BETA1-4 : bond 0.01042 ( 6) link_BETA1-4 : angle 2.42304 ( 18) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 1.58976 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.6068 (ptp) REVERT: A 272 MET cc_start: 0.7702 (mtp) cc_final: 0.7230 (mtp) REVERT: A 400 MET cc_start: 0.8297 (ptm) cc_final: 0.8034 (ptp) REVERT: B 94 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7375 (ppp) REVERT: B 392 VAL cc_start: 0.8694 (t) cc_final: 0.8479 (p) REVERT: B 394 MET cc_start: 0.4782 (ppp) cc_final: 0.4423 (ppp) REVERT: E 111 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7761 (p) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.0942 time to fit residues: 8.7298 Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101197 restraints weight = 21077.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103997 restraints weight = 11704.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105905 restraints weight = 7717.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107244 restraints weight = 5674.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108131 restraints weight = 4512.827| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9421 Z= 0.119 Angle : 0.540 11.445 12813 Z= 0.268 Chirality : 0.045 0.241 1456 Planarity : 0.003 0.033 1648 Dihedral : 5.047 44.650 1620 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 9.24 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1174 helix: 0.86 (0.59), residues: 90 sheet: 0.78 (0.24), residues: 439 loop : -0.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.010 0.001 TYR A 112 PHE 0.011 0.001 PHE A 477 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9395) covalent geometry : angle 0.52751 (12744) SS BOND : bond 0.00163 ( 9) SS BOND : angle 0.55764 ( 18) hydrogen bonds : bond 0.02868 ( 332) hydrogen bonds : angle 5.71508 ( 873) link_ALPHA1-2 : bond 0.00565 ( 1) link_ALPHA1-2 : angle 1.56106 ( 3) link_ALPHA1-3 : bond 0.01079 ( 1) link_ALPHA1-3 : angle 2.00360 ( 3) link_ALPHA1-6 : bond 0.00945 ( 1) link_ALPHA1-6 : angle 1.32187 ( 3) link_BETA1-4 : bond 0.01057 ( 6) link_BETA1-4 : angle 2.34789 ( 18) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.50663 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7618 (mtp) cc_final: 0.7203 (mtp) REVERT: A 400 MET cc_start: 0.8309 (ptm) cc_final: 0.8055 (ptp) REVERT: B 94 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7590 (ppp) REVERT: B 394 MET cc_start: 0.4940 (ppp) cc_final: 0.4734 (ppp) REVERT: F 99 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8150 (ttpp) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.1012 time to fit residues: 9.3366 Evaluate side-chains 56 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098110 restraints weight = 21256.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100762 restraints weight = 12597.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101438 restraints weight = 7961.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101348 restraints weight = 7366.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101536 restraints weight = 7076.721| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9421 Z= 0.240 Angle : 0.654 10.455 12813 Z= 0.332 Chirality : 0.047 0.229 1456 Planarity : 0.004 0.046 1648 Dihedral : 5.499 42.130 1620 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.04 % Allowed : 9.56 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.08 (0.24), residues: 1174 helix: 0.64 (0.59), residues: 90 sheet: 0.24 (0.23), residues: 469 loop : -0.30 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 64 TYR 0.020 0.002 TYR A 112 PHE 0.013 0.002 PHE F 107 TRP 0.020 0.002 TRP E 47 HIS 0.017 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 9395) covalent geometry : angle 0.63483 (12744) SS BOND : bond 0.00338 ( 9) SS BOND : angle 2.48554 ( 18) hydrogen bonds : bond 0.03599 ( 332) hydrogen bonds : angle 6.06848 ( 873) link_ALPHA1-2 : bond 0.00503 ( 1) link_ALPHA1-2 : angle 1.74053 ( 3) link_ALPHA1-3 : bond 0.01079 ( 1) link_ALPHA1-3 : angle 1.64866 ( 3) link_ALPHA1-6 : bond 0.00896 ( 1) link_ALPHA1-6 : angle 1.22561 ( 3) link_BETA1-4 : bond 0.01031 ( 6) link_BETA1-4 : angle 2.58888 ( 18) link_NAG-ASN : bond 0.00564 ( 8) link_NAG-ASN : angle 1.98205 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7616 (mtp) cc_final: 0.7208 (mtp) REVERT: A 400 MET cc_start: 0.8401 (ptm) cc_final: 0.8178 (ptp) REVERT: A 524 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 94 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7629 (ppp) REVERT: F 87 SER cc_start: 0.6281 (m) cc_final: 0.5898 (t) outliers start: 19 outliers final: 14 residues processed: 62 average time/residue: 0.0905 time to fit residues: 8.1378 Evaluate side-chains 57 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.117398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098940 restraints weight = 21128.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101505 restraints weight = 12249.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103284 restraints weight = 8311.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104457 restraints weight = 6279.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105199 restraints weight = 5126.497| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9421 Z= 0.161 Angle : 0.576 10.973 12813 Z= 0.289 Chirality : 0.046 0.220 1456 Planarity : 0.004 0.041 1648 Dihedral : 5.266 40.568 1620 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.83 % Allowed : 9.99 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.05 (0.24), residues: 1174 helix: 0.75 (0.59), residues: 90 sheet: 0.28 (0.23), residues: 454 loop : -0.31 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.014 0.001 TYR A 112 PHE 0.020 0.001 PHE B 388 TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9395) covalent geometry : angle 0.56129 (12744) SS BOND : bond 0.00233 ( 9) SS BOND : angle 1.65792 ( 18) hydrogen bonds : bond 0.03204 ( 332) hydrogen bonds : angle 5.92392 ( 873) link_ALPHA1-2 : bond 0.00603 ( 1) link_ALPHA1-2 : angle 1.59613 ( 3) link_ALPHA1-3 : bond 0.01113 ( 1) link_ALPHA1-3 : angle 1.83629 ( 3) link_ALPHA1-6 : bond 0.01001 ( 1) link_ALPHA1-6 : angle 1.18633 ( 3) link_BETA1-4 : bond 0.01042 ( 6) link_BETA1-4 : angle 2.37287 ( 18) link_NAG-ASN : bond 0.00317 ( 8) link_NAG-ASN : angle 1.69700 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7606 (mtp) cc_final: 0.7258 (mtp) REVERT: A 400 MET cc_start: 0.8330 (ptm) cc_final: 0.8113 (ptp) REVERT: A 524 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7433 (m-40) REVERT: B 94 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7314 (ppp) REVERT: B 117 MET cc_start: 0.8832 (tpp) cc_final: 0.8395 (mpp) REVERT: F 34 ASP cc_start: 0.8677 (t0) cc_final: 0.8363 (t0) outliers start: 17 outliers final: 12 residues processed: 62 average time/residue: 0.1047 time to fit residues: 9.3296 Evaluate side-chains 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.115871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098410 restraints weight = 21201.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100698 restraints weight = 12700.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101278 restraints weight = 8382.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101787 restraints weight = 7344.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101914 restraints weight = 6992.747| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9421 Z= 0.208 Angle : 0.628 12.319 12813 Z= 0.315 Chirality : 0.047 0.206 1456 Planarity : 0.004 0.044 1648 Dihedral : 5.462 43.694 1620 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.72 % Allowed : 10.53 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.24 (0.24), residues: 1174 helix: 0.61 (0.58), residues: 90 sheet: 0.12 (0.23), residues: 458 loop : -0.41 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.018 0.001 TYR A 112 PHE 0.014 0.001 PHE B 388 TRP 0.019 0.002 TRP E 47 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9395) covalent geometry : angle 0.61236 (12744) SS BOND : bond 0.00306 ( 9) SS BOND : angle 1.53916 ( 18) hydrogen bonds : bond 0.03482 ( 332) hydrogen bonds : angle 6.08053 ( 873) link_ALPHA1-2 : bond 0.00640 ( 1) link_ALPHA1-2 : angle 1.69645 ( 3) link_ALPHA1-3 : bond 0.01005 ( 1) link_ALPHA1-3 : angle 1.65601 ( 3) link_ALPHA1-6 : bond 0.00934 ( 1) link_ALPHA1-6 : angle 1.18352 ( 3) link_BETA1-4 : bond 0.01045 ( 6) link_BETA1-4 : angle 2.50033 ( 18) link_NAG-ASN : bond 0.00548 ( 8) link_NAG-ASN : angle 1.94263 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7633 (mtp) cc_final: 0.7310 (mtp) REVERT: A 524 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7340 (m-40) REVERT: B 94 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7154 (ppp) REVERT: F 34 ASP cc_start: 0.8710 (t0) cc_final: 0.8414 (t0) REVERT: F 87 SER cc_start: 0.6361 (m) cc_final: 0.5994 (t) outliers start: 16 outliers final: 14 residues processed: 64 average time/residue: 0.0964 time to fit residues: 8.8254 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.116081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097487 restraints weight = 21008.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100023 restraints weight = 12381.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101706 restraints weight = 8481.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.102899 restraints weight = 6477.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103695 restraints weight = 5300.299| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9421 Z= 0.203 Angle : 0.617 12.105 12813 Z= 0.310 Chirality : 0.046 0.195 1456 Planarity : 0.004 0.046 1648 Dihedral : 5.515 46.075 1620 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -0.34 (0.24), residues: 1174 helix: 0.42 (0.58), residues: 92 sheet: 0.06 (0.23), residues: 458 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.017 0.001 TYR A 112 PHE 0.014 0.001 PHE B 388 TRP 0.020 0.002 TRP E 47 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9395) covalent geometry : angle 0.60297 (12744) SS BOND : bond 0.00307 ( 9) SS BOND : angle 1.43055 ( 18) hydrogen bonds : bond 0.03448 ( 332) hydrogen bonds : angle 6.12269 ( 873) link_ALPHA1-2 : bond 0.00671 ( 1) link_ALPHA1-2 : angle 1.70661 ( 3) link_ALPHA1-3 : bond 0.01011 ( 1) link_ALPHA1-3 : angle 1.67154 ( 3) link_ALPHA1-6 : bond 0.00913 ( 1) link_ALPHA1-6 : angle 1.16472 ( 3) link_BETA1-4 : bond 0.01024 ( 6) link_BETA1-4 : angle 2.40903 ( 18) link_NAG-ASN : bond 0.00462 ( 8) link_NAG-ASN : angle 1.85302 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.99 seconds wall clock time: 26 minutes 46.24 seconds (1606.24 seconds total)