Starting phenix.real_space_refine on Sun Jul 27 14:03:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_20796.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_20796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_20796.map" model { file = "/net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_20796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujc_20796/07_2025/6ujc_20796.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} 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: 6.39, per 1000 atoms: 0.69 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: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.49 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: 3.81 Time building geometry restraints manager: 3.69 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: 2.790 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.020 0.006 TRP B 308 HIS 0.005 0.001 HIS A 521 PHE 0.024 0.004 PHE A 276 TYR 0.030 0.005 TYR B 103 ARG 0.005 0.001 ARG F 32 Details of bonding type rmsd link_NAG-ASN : bond 0.06459 ( 8) link_NAG-ASN : angle 2.15531 ( 24) 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_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) hydrogen bonds : bond 0.16567 ( 332) hydrogen bonds : angle 9.04010 ( 873) SS BOND : bond 0.04336 ( 9) SS BOND : angle 2.07281 ( 18) covalent geometry : bond 0.01379 ( 9395) covalent geometry : angle 1.39568 (12744) *********************** 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 : 0.987 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: 0.2653 time to fit residues: 56.9577 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 : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.123219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105440 restraints weight = 20841.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108340 restraints weight = 11195.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110310 restraints weight = 7231.044| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9421 Z= 0.164 Angle : 0.673 14.618 12813 Z= 0.342 Chirality : 0.048 0.164 1456 Planarity : 0.004 0.056 1648 Dihedral : 7.593 86.237 1620 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1174 helix: 0.02 (0.53), residues: 90 sheet: 0.80 (0.22), residues: 465 loop : 0.14 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS B 118 PHE 0.017 0.002 PHE A 276 TYR 0.015 0.002 TYR A 265 ARG 0.007 0.001 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 8) link_NAG-ASN : angle 2.11194 ( 24) link_ALPHA1-6 : bond 0.00897 ( 1) link_ALPHA1-6 : angle 1.48905 ( 3) link_BETA1-4 : bond 0.01235 ( 6) link_BETA1-4 : angle 3.21683 ( 18) link_ALPHA1-2 : bond 0.00348 ( 1) link_ALPHA1-2 : angle 1.53158 ( 3) link_ALPHA1-3 : bond 0.01194 ( 1) link_ALPHA1-3 : angle 1.44150 ( 3) hydrogen bonds : bond 0.04099 ( 332) hydrogen bonds : angle 7.01496 ( 873) SS BOND : bond 0.00540 ( 9) SS BOND : angle 2.26756 ( 18) covalent geometry : bond 0.00366 ( 9395) covalent geometry : angle 0.65058 (12744) *********************** 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 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8201 (ptm) cc_final: 0.7808 (ptp) REVERT: B 117 MET cc_start: 0.8463 (mmm) cc_final: 0.8188 (tpp) REVERT: B 392 VAL cc_start: 0.8699 (t) cc_final: 0.8463 (p) REVERT: E 52 ASN cc_start: 0.7395 (t0) cc_final: 0.6948 (t0) REVERT: F 100 GLN cc_start: 0.8543 (pp30) cc_final: 0.8338 (pp30) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.2489 time to fit residues: 32.4605 Evaluate side-chains 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU 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 5 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.120249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102309 restraints weight = 21142.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105050 restraints weight = 11822.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106945 restraints weight = 7816.527| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9421 Z= 0.165 Angle : 0.623 12.846 12813 Z= 0.314 Chirality : 0.047 0.204 1456 Planarity : 0.004 0.028 1648 Dihedral : 6.415 66.710 1620 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.61 % Allowed : 7.30 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1174 helix: 0.32 (0.56), residues: 89 sheet: 0.63 (0.23), residues: 459 loop : 0.01 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS B 166 PHE 0.013 0.001 PHE A 477 TYR 0.023 0.001 TYR A 265 ARG 0.004 0.001 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 8) link_NAG-ASN : angle 1.75453 ( 24) link_ALPHA1-6 : bond 0.01106 ( 1) link_ALPHA1-6 : angle 1.38484 ( 3) link_BETA1-4 : bond 0.01475 ( 6) link_BETA1-4 : angle 2.69484 ( 18) link_ALPHA1-2 : bond 0.00622 ( 1) link_ALPHA1-2 : angle 1.27979 ( 3) link_ALPHA1-3 : bond 0.01234 ( 1) link_ALPHA1-3 : angle 1.39892 ( 3) hydrogen bonds : bond 0.03661 ( 332) hydrogen bonds : angle 6.42734 ( 873) SS BOND : bond 0.00226 ( 9) SS BOND : angle 1.03230 ( 18) covalent geometry : bond 0.00369 ( 9395) covalent geometry : angle 0.60934 (12744) *********************** 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 77 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8332 (ptm) cc_final: 0.8113 (ptp) REVERT: B 94 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7219 (ppp) REVERT: B 110 LEU cc_start: 0.8920 (tp) cc_final: 0.8591 (tt) REVERT: B 271 VAL cc_start: 0.8868 (t) cc_final: 0.8656 (p) REVERT: E 52 ASN cc_start: 0.7435 (t0) cc_final: 0.7074 (t0) REVERT: E 111 THR cc_start: 0.7802 (m) cc_final: 0.7594 (p) REVERT: F 21 MET cc_start: 0.7584 (ptp) cc_final: 0.7274 (ptp) REVERT: F 100 GLN cc_start: 0.8631 (pp30) cc_final: 0.8390 (pp30) outliers start: 15 outliers final: 9 residues processed: 70 average time/residue: 0.2199 time to fit residues: 22.1912 Evaluate side-chains 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 94 MET 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 Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.118730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100247 restraints weight = 21134.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103047 restraints weight = 11756.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104949 restraints weight = 7743.547| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9421 Z= 0.158 Angle : 0.581 12.464 12813 Z= 0.291 Chirality : 0.046 0.255 1456 Planarity : 0.004 0.035 1648 Dihedral : 5.785 56.048 1620 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.04 % Allowed : 7.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1174 helix: 0.44 (0.58), residues: 90 sheet: 0.74 (0.24), residues: 448 loop : -0.05 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS B 166 PHE 0.010 0.001 PHE A 276 TYR 0.014 0.001 TYR A 112 ARG 0.004 0.000 ARG B 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 8) link_NAG-ASN : angle 1.76170 ( 24) link_ALPHA1-6 : bond 0.00936 ( 1) link_ALPHA1-6 : angle 1.42436 ( 3) link_BETA1-4 : bond 0.01082 ( 6) link_BETA1-4 : angle 2.63124 ( 18) link_ALPHA1-2 : bond 0.00452 ( 1) link_ALPHA1-2 : angle 1.63794 ( 3) link_ALPHA1-3 : bond 0.01178 ( 1) link_ALPHA1-3 : angle 1.82786 ( 3) hydrogen bonds : bond 0.03293 ( 332) hydrogen bonds : angle 6.10326 ( 873) SS BOND : bond 0.00235 ( 9) SS BOND : angle 0.98613 ( 18) covalent geometry : bond 0.00357 ( 9395) covalent geometry : angle 0.56599 (12744) *********************** 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 79 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8441 (ptm) cc_final: 0.8150 (ptp) REVERT: B 94 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7278 (ppp) REVERT: E 52 ASN cc_start: 0.7556 (t0) cc_final: 0.7238 (t0) REVERT: E 111 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7579 (p) REVERT: F 87 SER cc_start: 0.5902 (m) cc_final: 0.5410 (t) REVERT: F 99 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8269 (ttpp) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 0.2287 time to fit residues: 22.8935 Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 ARG 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 174 LEU Chi-restraints excluded: chain B residue 319 THR 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 4 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.119201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100390 restraints weight = 21106.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103181 restraints weight = 11798.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105096 restraints weight = 7801.153| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3708 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= 0.137 Angle : 0.558 12.007 12813 Z= 0.279 Chirality : 0.046 0.258 1456 Planarity : 0.004 0.037 1648 Dihedral : 5.436 49.646 1620 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.29 % Allowed : 9.24 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1174 helix: 0.53 (0.58), residues: 90 sheet: 0.72 (0.24), residues: 452 loop : -0.17 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS B 166 PHE 0.012 0.001 PHE A 477 TYR 0.012 0.001 TYR A 112 ARG 0.004 0.000 ARG B 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 8) link_NAG-ASN : angle 1.56707 ( 24) link_ALPHA1-6 : bond 0.01057 ( 1) link_ALPHA1-6 : angle 1.37909 ( 3) link_BETA1-4 : bond 0.01100 ( 6) link_BETA1-4 : angle 2.44179 ( 18) link_ALPHA1-2 : bond 0.00557 ( 1) link_ALPHA1-2 : angle 1.45342 ( 3) link_ALPHA1-3 : bond 0.01077 ( 1) link_ALPHA1-3 : angle 1.88351 ( 3) hydrogen bonds : bond 0.03134 ( 332) hydrogen bonds : angle 5.90102 ( 873) SS BOND : bond 0.00193 ( 9) SS BOND : angle 0.66902 ( 18) covalent geometry : bond 0.00308 ( 9395) covalent geometry : angle 0.54517 (12744) *********************** 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 72 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8014 (mtp) cc_final: 0.7757 (mtp) REVERT: A 400 MET cc_start: 0.8396 (ptm) cc_final: 0.8101 (ptp) REVERT: B 94 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7292 (ppp) REVERT: B 117 MET cc_start: 0.8905 (tpp) cc_final: 0.8461 (mpp) REVERT: B 394 MET cc_start: 0.5118 (ppp) cc_final: 0.4786 (ppp) REVERT: E 52 ASN cc_start: 0.7594 (t0) cc_final: 0.7255 (t0) REVERT: E 111 THR cc_start: 0.8011 (m) cc_final: 0.7776 (p) REVERT: F 87 SER cc_start: 0.5971 (m) cc_final: 0.5473 (t) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.2891 time to fit residues: 28.9567 Evaluate side-chains 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP 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 174 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.0020 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 107 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 overall best weight: 0.2344 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.120572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102560 restraints weight = 20895.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105200 restraints weight = 11870.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.106994 restraints weight = 7944.510| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9421 Z= 0.095 Angle : 0.530 11.677 12813 Z= 0.264 Chirality : 0.045 0.250 1456 Planarity : 0.003 0.031 1648 Dihedral : 5.121 46.502 1620 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.50 % Allowed : 9.02 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1174 helix: 0.70 (0.59), residues: 90 sheet: 0.74 (0.24), residues: 441 loop : -0.17 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.002 0.000 HIS A 113 PHE 0.009 0.001 PHE A 477 TYR 0.011 0.001 TYR F 59 ARG 0.003 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 8) link_NAG-ASN : angle 1.42453 ( 24) link_ALPHA1-6 : bond 0.01139 ( 1) link_ALPHA1-6 : angle 1.38734 ( 3) link_BETA1-4 : bond 0.01092 ( 6) link_BETA1-4 : angle 2.33974 ( 18) link_ALPHA1-2 : bond 0.00539 ( 1) link_ALPHA1-2 : angle 1.49415 ( 3) link_ALPHA1-3 : bond 0.01078 ( 1) link_ALPHA1-3 : angle 2.07260 ( 3) hydrogen bonds : bond 0.02850 ( 332) hydrogen bonds : angle 5.69946 ( 873) SS BOND : bond 0.00148 ( 9) SS BOND : angle 0.52603 ( 18) covalent geometry : bond 0.00206 ( 9395) covalent geometry : angle 0.51784 (12744) *********************** 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 68 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8359 (ptm) cc_final: 0.8082 (ptp) REVERT: A 524 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7438 (m-40) REVERT: B 94 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7273 (ppp) REVERT: B 394 MET cc_start: 0.4910 (ppp) cc_final: 0.4626 (ppp) REVERT: E 52 ASN cc_start: 0.7545 (t0) cc_final: 0.7217 (t0) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.2406 time to fit residues: 21.4069 Evaluate side-chains 58 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP 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 174 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.115707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098220 restraints weight = 21245.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100446 restraints weight = 12752.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101187 restraints weight = 9699.216| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 9421 Z= 0.251 Angle : 0.656 10.545 12813 Z= 0.334 Chirality : 0.048 0.238 1456 Planarity : 0.004 0.040 1648 Dihedral : 5.599 42.969 1620 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.15 % Allowed : 9.24 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1174 helix: 0.50 (0.58), residues: 90 sheet: 0.30 (0.23), residues: 465 loop : -0.41 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.005 0.001 HIS B 166 PHE 0.013 0.002 PHE F 107 TYR 0.021 0.002 TYR A 112 ARG 0.003 0.001 ARG B 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 8) link_NAG-ASN : angle 2.00290 ( 24) link_ALPHA1-6 : bond 0.00903 ( 1) link_ALPHA1-6 : angle 1.29341 ( 3) link_BETA1-4 : bond 0.01058 ( 6) link_BETA1-4 : angle 2.65041 ( 18) link_ALPHA1-2 : bond 0.00561 ( 1) link_ALPHA1-2 : angle 1.66743 ( 3) link_ALPHA1-3 : bond 0.01180 ( 1) link_ALPHA1-3 : angle 1.72091 ( 3) hydrogen bonds : bond 0.03743 ( 332) hydrogen bonds : angle 6.12537 ( 873) SS BOND : bond 0.00325 ( 9) SS BOND : angle 0.94532 ( 18) covalent geometry : bond 0.00573 ( 9395) covalent geometry : angle 0.64198 (12744) *********************** 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 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8452 (ptm) cc_final: 0.8210 (ptp) REVERT: A 524 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: B 94 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7178 (ppp) REVERT: B 407 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8505 (tp) REVERT: E 52 ASN cc_start: 0.7511 (t0) cc_final: 0.7301 (t0) REVERT: F 34 ASP cc_start: 0.8769 (t0) cc_final: 0.8539 (t0) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.2544 time to fit residues: 23.2965 Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 219 ASP 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 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 B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.117825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099419 restraints weight = 21353.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102060 restraints weight = 12249.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103863 restraints weight = 8251.143| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9421 Z= 0.125 Angle : 0.558 11.152 12813 Z= 0.282 Chirality : 0.046 0.231 1456 Planarity : 0.003 0.031 1648 Dihedral : 5.236 41.897 1620 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 9.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1174 helix: 0.66 (0.59), residues: 92 sheet: 0.38 (0.24), residues: 449 loop : -0.37 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.007 0.001 HIS B 266 PHE 0.017 0.001 PHE B 388 TYR 0.012 0.001 TYR A 112 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 8) link_NAG-ASN : angle 1.56333 ( 24) link_ALPHA1-6 : bond 0.01034 ( 1) link_ALPHA1-6 : angle 1.24316 ( 3) link_BETA1-4 : bond 0.01058 ( 6) link_BETA1-4 : angle 2.35693 ( 18) link_ALPHA1-2 : bond 0.00603 ( 1) link_ALPHA1-2 : angle 1.50909 ( 3) link_ALPHA1-3 : bond 0.01187 ( 1) link_ALPHA1-3 : angle 2.02084 ( 3) hydrogen bonds : bond 0.03121 ( 332) hydrogen bonds : angle 5.88476 ( 873) SS BOND : bond 0.00275 ( 9) SS BOND : angle 1.63412 ( 18) covalent geometry : bond 0.00281 ( 9395) covalent geometry : angle 0.54321 (12744) *********************** 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 74 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8378 (ptm) cc_final: 0.8154 (ptp) REVERT: A 524 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: B 94 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7373 (ppp) REVERT: B 117 MET cc_start: 0.8814 (tpp) cc_final: 0.8369 (tpp) REVERT: B 407 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 52 ASN cc_start: 0.7717 (t0) cc_final: 0.7428 (t0) REVERT: F 34 ASP cc_start: 0.8753 (t0) cc_final: 0.8522 (t0) outliers start: 23 outliers final: 18 residues processed: 70 average time/residue: 0.2417 time to fit residues: 24.6876 Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 261 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 398 ARG 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 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 319 THR 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 B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.115283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096788 restraints weight = 21072.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099284 restraints weight = 12447.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100993 restraints weight = 8560.816| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9421 Z= 0.244 Angle : 0.654 10.485 12813 Z= 0.332 Chirality : 0.048 0.215 1456 Planarity : 0.004 0.041 1648 Dihedral : 5.602 42.803 1620 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.36 % Allowed : 9.77 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1174 helix: 0.43 (0.57), residues: 92 sheet: 0.21 (0.24), residues: 455 loop : -0.54 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.002 PHE A 477 TYR 0.020 0.002 TYR A 112 ARG 0.004 0.001 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 8) link_NAG-ASN : angle 2.01628 ( 24) link_ALPHA1-6 : bond 0.00908 ( 1) link_ALPHA1-6 : angle 1.22537 ( 3) link_BETA1-4 : bond 0.01051 ( 6) link_BETA1-4 : angle 2.58456 ( 18) link_ALPHA1-2 : bond 0.00603 ( 1) link_ALPHA1-2 : angle 1.76298 ( 3) link_ALPHA1-3 : bond 0.01090 ( 1) link_ALPHA1-3 : angle 1.66003 ( 3) hydrogen bonds : bond 0.03783 ( 332) hydrogen bonds : angle 6.19731 ( 873) SS BOND : bond 0.00377 ( 9) SS BOND : angle 1.73121 ( 18) covalent geometry : bond 0.00560 ( 9395) covalent geometry : angle 0.63765 (12744) *********************** 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 72 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8410 (ptm) cc_final: 0.8199 (ptp) REVERT: A 524 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: B 94 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7361 (ppp) REVERT: B 407 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8537 (tp) REVERT: F 34 ASP cc_start: 0.8733 (t0) cc_final: 0.8427 (t0) outliers start: 22 outliers final: 17 residues processed: 69 average time/residue: 0.2262 time to fit residues: 22.5402 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 219 ASP 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 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 319 THR 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 B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU 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 40 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 103 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099426 restraints weight = 20942.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101936 restraints weight = 12127.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103633 restraints weight = 8228.681| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9421 Z= 0.102 Angle : 0.541 12.226 12813 Z= 0.272 Chirality : 0.045 0.206 1456 Planarity : 0.004 0.040 1648 Dihedral : 5.109 43.265 1620 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.61 % Allowed : 10.42 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1174 helix: 0.76 (0.59), residues: 92 sheet: 0.36 (0.24), residues: 447 loop : -0.46 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS B 63 PHE 0.011 0.001 PHE B 388 TYR 0.012 0.001 TYR F 59 ARG 0.010 0.000 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.38885 ( 24) link_ALPHA1-6 : bond 0.01008 ( 1) link_ALPHA1-6 : angle 1.20438 ( 3) link_BETA1-4 : bond 0.01141 ( 6) link_BETA1-4 : angle 2.23211 ( 18) link_ALPHA1-2 : bond 0.00638 ( 1) link_ALPHA1-2 : angle 1.44446 ( 3) link_ALPHA1-3 : bond 0.01102 ( 1) link_ALPHA1-3 : angle 2.08783 ( 3) hydrogen bonds : bond 0.02946 ( 332) hydrogen bonds : angle 5.82493 ( 873) SS BOND : bond 0.00168 ( 9) SS BOND : angle 1.10485 ( 18) covalent geometry : bond 0.00222 ( 9395) covalent geometry : angle 0.52965 (12744) ********************** 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: 15 poor density : 52 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8400 (ptm) cc_final: 0.8024 (ptp) REVERT: A 524 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7446 (m-40) REVERT: B 94 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7410 (ppp) REVERT: B 117 MET cc_start: 0.8763 (tpp) cc_final: 0.8443 (tpp) REVERT: B 407 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8540 (tp) REVERT: F 34 ASP cc_start: 0.8681 (t0) cc_final: 0.8423 (t0) outliers start: 15 outliers final: 12 residues processed: 64 average time/residue: 0.2045 time to fit residues: 19.2127 Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 219 ASP 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 199 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 B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.0040 chunk 50 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.118045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100467 restraints weight = 21157.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103492 restraints weight = 12751.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103946 restraints weight = 7566.878| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9421 Z= 0.124 Angle : 0.544 11.387 12813 Z= 0.272 Chirality : 0.045 0.195 1456 Planarity : 0.003 0.030 1648 Dihedral : 5.013 42.851 1620 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.72 % Allowed : 10.42 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1174 helix: 0.80 (0.59), residues: 92 sheet: 0.39 (0.24), residues: 443 loop : -0.42 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.001 HIS B 63 PHE 0.011 0.001 PHE A 477 TYR 0.012 0.001 TYR A 435 ARG 0.008 0.000 ARG B 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 8) link_NAG-ASN : angle 1.49583 ( 24) link_ALPHA1-6 : bond 0.00916 ( 1) link_ALPHA1-6 : angle 1.22595 ( 3) link_BETA1-4 : bond 0.01065 ( 6) link_BETA1-4 : angle 2.31689 ( 18) link_ALPHA1-2 : bond 0.00646 ( 1) link_ALPHA1-2 : angle 1.60707 ( 3) link_ALPHA1-3 : bond 0.00956 ( 1) link_ALPHA1-3 : angle 1.83930 ( 3) hydrogen bonds : bond 0.03012 ( 332) hydrogen bonds : angle 5.75199 ( 873) SS BOND : bond 0.00168 ( 9) SS BOND : angle 1.33005 ( 18) covalent geometry : bond 0.00282 ( 9395) covalent geometry : angle 0.53075 (12744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.07 seconds wall clock time: 54 minutes 44.22 seconds (3284.22 seconds total)