Starting phenix.real_space_refine on Wed May 14 18:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.map" model { file = "/net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oe0_16821/05_2025/8oe0_16821.cif" } resolution = 4.6 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7524 2.51 5 N 2096 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2323 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3852 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4477 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 531} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.85, per 1000 atoms: 0.57 Number of scatterers: 11980 At special positions: 0 Unit cell: (95.13, 137.41, 197.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2279 8.00 N 2096 7.00 C 7524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 405 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.04 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 144 " " NAG D 801 " - " ASN D 224 " " NAG E 1 " - " ASN B 220 " " NAG F 1 " - " ASN C 463 " Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 34 sheets defined 8.9% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 4.247A pdb=" N GLN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.554A pdb=" N CYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.583A pdb=" N CYS A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.776A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 463 through 468 removed outlier: 4.072A pdb=" N ALA C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 234 through 237 No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.875A pdb=" N GLU D 563 " --> pdb=" O PRO D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27 removed outlier: 5.509A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 33 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 35 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 107 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 92 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 27 removed outlier: 5.509A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 33 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 35 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 107 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.170A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.170A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 185 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 54 removed outlier: 6.235A pdb=" N ASP C 68 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN C 50 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 66 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 106 " --> pdb=" O CYS C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.860A pdb=" N ASN C 121 " --> pdb=" O CYS C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.860A pdb=" N ASN C 121 " --> pdb=" O CYS C 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB5, first strand: chain 'C' and resid 189 through 193 Processing sheet with id=AB6, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AB7, first strand: chain 'C' and resid 320 through 324 removed outlier: 3.951A pdb=" N LYS C 303 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA C 342 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C 350 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB9, first strand: chain 'C' and resid 405 through 408 removed outlier: 3.866A pdb=" N LEU C 455 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 453 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 474 through 477 Processing sheet with id=AC2, first strand: chain 'C' and resid 514 through 519 removed outlier: 7.156A pdb=" N ASP C 544 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 514 through 519 removed outlier: 3.843A pdb=" N GLN C 540 " --> pdb=" O ARG C 505 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 507 " --> pdb=" O LYS C 538 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 538 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 42 removed outlier: 3.534A pdb=" N GLY D 134 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 72 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 80 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 74 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 196 through 198 removed outlier: 4.456A pdb=" N ASN D 159 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN D 142 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE D 239 " --> pdb=" O CYS D 145 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN D 147 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 188 Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 250 removed outlier: 3.831A pdb=" N ILE D 246 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN D 261 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 248 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 259 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 289 Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 348 removed outlier: 3.600A pdb=" N GLN D 348 " --> pdb=" O GLN D 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 387 through 393 removed outlier: 4.425A pdb=" N THR D 387 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP D 408 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 415 through 416 removed outlier: 3.631A pdb=" N GLY D 419 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.645A pdb=" N GLU D 447 " --> pdb=" O ASN D 451 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 488 through 491 Processing sheet with id=AD6, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AD7, first strand: chain 'D' and resid 585 through 590 442 hydrogen bonds defined for protein. 1146 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: 4.10 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3851 1.34 - 1.46: 2833 1.46 - 1.59: 5466 1.59 - 1.72: 0 1.72 - 1.84: 111 Bond restraints: 12261 Sorted by residual: bond pdb=" N VAL B 249 " pdb=" CA VAL B 249 " ideal model delta sigma weight residual 1.461 1.505 -0.045 1.22e-02 6.72e+03 1.35e+01 bond pdb=" N VAL D 238 " pdb=" CA VAL D 238 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N VAL C 74 " pdb=" CA VAL C 74 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.04e-02 9.25e+03 1.02e+01 bond pdb=" N THR C 146 " pdb=" CA THR C 146 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.72e+00 ... (remaining 12256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16039 2.27 - 4.53: 545 4.53 - 6.80: 57 6.80 - 9.06: 15 9.06 - 11.33: 4 Bond angle restraints: 16660 Sorted by residual: angle pdb=" N SER B 171 " pdb=" CA SER B 171 " pdb=" C SER B 171 " ideal model delta sigma weight residual 112.92 104.81 8.11 1.23e+00 6.61e-01 4.34e+01 angle pdb=" N VAL D 238 " pdb=" CA VAL D 238 " pdb=" C VAL D 238 " ideal model delta sigma weight residual 108.89 116.19 -7.30 1.32e+00 5.74e-01 3.06e+01 angle pdb=" N THR C 146 " pdb=" CA THR C 146 " pdb=" C THR C 146 " ideal model delta sigma weight residual 109.96 117.87 -7.91 1.50e+00 4.44e-01 2.78e+01 angle pdb=" CA PRO D 506 " pdb=" N PRO D 506 " pdb=" CD PRO D 506 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA GLN B 248 " pdb=" C GLN B 248 " pdb=" O GLN B 248 " ideal model delta sigma weight residual 121.36 116.33 5.03 1.06e+00 8.90e-01 2.25e+01 ... (remaining 16655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 6954 21.59 - 43.19: 494 43.19 - 64.78: 70 64.78 - 86.38: 31 86.38 - 107.97: 5 Dihedral angle restraints: 7554 sinusoidal: 3184 harmonic: 4370 Sorted by residual: dihedral pdb=" CB CYS C 252 " pdb=" SG CYS C 252 " pdb=" SG CYS C 293 " pdb=" CB CYS C 293 " ideal model delta sinusoidal sigma weight residual 93.00 -176.88 -90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS C 315 " pdb=" SG CYS C 315 " pdb=" SG CYS C 405 " pdb=" CB CYS C 405 " ideal model delta sinusoidal sigma weight residual 93.00 173.52 -80.52 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -161.75 75.75 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1727 0.100 - 0.201: 124 0.201 - 0.301: 22 0.301 - 0.401: 0 0.401 - 0.502: 1 Chirality restraints: 1874 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 220 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CA CYS C 80 " pdb=" N CYS C 80 " pdb=" C CYS C 80 " pdb=" CB CYS C 80 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1871 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " -0.237 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" C7 NAG C 602 " 0.061 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " 0.340 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 67 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C HIS A 67 " -0.068 2.00e-02 2.50e+03 pdb=" O HIS A 67 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU A 68 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 78 " 0.017 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU C 78 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 78 " 0.026 2.00e-02 2.50e+03 pdb=" N TRP C 79 " 0.022 2.00e-02 2.50e+03 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 911 2.74 - 3.28: 11585 3.28 - 3.82: 19924 3.82 - 4.36: 22385 4.36 - 4.90: 37453 Nonbonded interactions: 92258 Sorted by model distance: nonbonded pdb=" OG SER B 159 " pdb=" OD1 ASP B 161 " model vdw 2.199 3.040 nonbonded pdb=" O ASP D 450 " pdb=" OG SER D 501 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 231 " pdb=" OG SER B 321 " model vdw 2.249 3.040 nonbonded pdb=" NZ LYS C 147 " pdb=" O TRP C 244 " model vdw 2.269 3.120 nonbonded pdb=" N MET B 23 " pdb=" O VAL B 32 " model vdw 2.269 3.120 ... (remaining 92253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.190 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 : 0.005 0.082 12291 Z= 0.300 Angle : 0.959 12.702 16728 Z= 0.550 Chirality : 0.058 0.502 1874 Planarity : 0.008 0.201 2122 Dihedral : 15.088 107.973 4646 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.37 % Allowed : 1.42 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.82 (0.21), residues: 1468 helix: 0.38 (0.52), residues: 105 sheet: 0.32 (0.21), residues: 600 loop : -1.42 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 398 HIS 0.005 0.001 HIS B 105 PHE 0.062 0.002 PHE A 134 TYR 0.029 0.001 TYR A 130 ARG 0.012 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 5) link_NAG-ASN : angle 5.72135 ( 15) link_BETA1-4 : bond 0.00874 ( 3) link_BETA1-4 : angle 4.55292 ( 9) hydrogen bonds : bond 0.11462 ( 416) hydrogen bonds : angle 7.12539 ( 1146) SS BOND : bond 0.00396 ( 22) SS BOND : angle 1.97523 ( 44) covalent geometry : bond 0.00483 (12261) covalent geometry : angle 0.93411 (16660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9543 (tt) cc_final: 0.9295 (tt) REVERT: A 65 ILE cc_start: 0.8301 (mp) cc_final: 0.8097 (tp) REVERT: A 67 HIS cc_start: 0.8387 (t-90) cc_final: 0.7995 (t70) REVERT: A 209 MET cc_start: 0.9541 (tmm) cc_final: 0.9286 (tpt) REVERT: B 27 GLU cc_start: 0.9068 (mp0) cc_final: 0.8784 (mm-30) REVERT: B 37 TRP cc_start: 0.8273 (t-100) cc_final: 0.7944 (t-100) REVERT: B 172 LEU cc_start: 0.9617 (mp) cc_final: 0.9314 (pp) REVERT: B 190 SER cc_start: 0.8474 (p) cc_final: 0.7970 (t) REVERT: B 204 LEU cc_start: 0.9248 (mm) cc_final: 0.8744 (pp) REVERT: B 215 GLN cc_start: 0.9527 (mm-40) cc_final: 0.9214 (tt0) REVERT: B 218 TYR cc_start: 0.8674 (t80) cc_final: 0.8296 (t80) REVERT: B 294 PHE cc_start: 0.8720 (p90) cc_final: 0.8319 (p90) REVERT: C 60 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: C 143 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 145 TRP cc_start: 0.8701 (t-100) cc_final: 0.8420 (t-100) REVERT: C 154 HIS cc_start: 0.7776 (m170) cc_final: 0.7411 (p90) REVERT: C 155 ILE cc_start: 0.8002 (pt) cc_final: 0.7345 (mt) REVERT: C 212 MET cc_start: 0.8715 (ptm) cc_final: 0.7967 (pmm) REVERT: C 223 MET cc_start: 0.8840 (pmm) cc_final: 0.8319 (pmm) REVERT: C 233 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6768 (tmm160) REVERT: C 280 MET cc_start: 0.9047 (mpp) cc_final: 0.7833 (tpt) REVERT: C 548 LEU cc_start: 0.6931 (mt) cc_final: 0.6647 (tp) REVERT: D 172 LEU cc_start: 0.9573 (mm) cc_final: 0.9184 (mm) REVERT: D 178 ASN cc_start: 0.8294 (t0) cc_final: 0.8072 (p0) REVERT: D 308 PHE cc_start: 0.8467 (m-10) cc_final: 0.7791 (m-10) REVERT: D 408 TRP cc_start: 0.8294 (m-90) cc_final: 0.7892 (m-90) REVERT: D 513 ARG cc_start: 0.7483 (tmm-80) cc_final: 0.7164 (tmm-80) outliers start: 5 outliers final: 0 residues processed: 251 average time/residue: 0.2526 time to fit residues: 87.8524 Evaluate side-chains 168 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN B 91 HIS C 355 HIS ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.108508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.082482 restraints weight = 62509.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084914 restraints weight = 42208.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086737 restraints weight = 31151.004| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12291 Z= 0.183 Angle : 0.702 12.012 16728 Z= 0.348 Chirality : 0.044 0.377 1874 Planarity : 0.005 0.050 2122 Dihedral : 7.233 59.203 1774 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.22 % Allowed : 6.79 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.75 (0.21), residues: 1468 helix: 0.25 (0.48), residues: 106 sheet: 0.31 (0.21), residues: 599 loop : -1.29 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 244 HIS 0.006 0.001 HIS A 146 PHE 0.036 0.002 PHE A 134 TYR 0.015 0.002 TYR C 143 ARG 0.006 0.001 ARG A 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 5) link_NAG-ASN : angle 5.25571 ( 15) link_BETA1-4 : bond 0.00516 ( 3) link_BETA1-4 : angle 3.08247 ( 9) hydrogen bonds : bond 0.04228 ( 416) hydrogen bonds : angle 6.11225 ( 1146) SS BOND : bond 0.00320 ( 22) SS BOND : angle 1.12793 ( 44) covalent geometry : bond 0.00386 (12261) covalent geometry : angle 0.67966 (16660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9604 (tt) cc_final: 0.9315 (tt) REVERT: A 42 LYS cc_start: 0.9716 (ptmm) cc_final: 0.9500 (ptmm) REVERT: A 159 ILE cc_start: 0.9085 (tp) cc_final: 0.8547 (tp) REVERT: A 163 MET cc_start: 0.8895 (mmt) cc_final: 0.8672 (mmm) REVERT: B 66 HIS cc_start: 0.8581 (t70) cc_final: 0.8379 (t70) REVERT: B 136 ARG cc_start: 0.7971 (ttt-90) cc_final: 0.7409 (tmt-80) REVERT: B 172 LEU cc_start: 0.9668 (mp) cc_final: 0.9339 (pp) REVERT: B 190 SER cc_start: 0.8877 (p) cc_final: 0.7872 (t) REVERT: B 215 GLN cc_start: 0.9601 (tp-100) cc_final: 0.9357 (tp-100) REVERT: B 218 TYR cc_start: 0.9091 (t80) cc_final: 0.8266 (t80) REVERT: B 294 PHE cc_start: 0.8667 (p90) cc_final: 0.8446 (p90) REVERT: C 50 ASN cc_start: 0.9018 (m-40) cc_final: 0.8742 (m110) REVERT: C 60 ASP cc_start: 0.8595 (m-30) cc_final: 0.8277 (m-30) REVERT: C 155 ILE cc_start: 0.8265 (pt) cc_final: 0.7705 (mt) REVERT: C 212 MET cc_start: 0.8768 (ptm) cc_final: 0.7988 (pmm) REVERT: C 223 MET cc_start: 0.8315 (pmm) cc_final: 0.7867 (pmm) REVERT: D 172 LEU cc_start: 0.9437 (mm) cc_final: 0.9085 (mm) REVERT: D 308 PHE cc_start: 0.8424 (m-10) cc_final: 0.7499 (m-10) REVERT: D 408 TRP cc_start: 0.8471 (m-90) cc_final: 0.7987 (m-90) outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.2258 time to fit residues: 63.6068 Evaluate side-chains 155 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN D 309 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.107994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081872 restraints weight = 63265.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084398 restraints weight = 42163.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086264 restraints weight = 30968.767| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12291 Z= 0.138 Angle : 0.651 11.892 16728 Z= 0.320 Chirality : 0.044 0.341 1874 Planarity : 0.005 0.076 2122 Dihedral : 6.568 57.355 1774 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.68 (0.21), residues: 1468 helix: 0.41 (0.49), residues: 107 sheet: 0.36 (0.21), residues: 599 loop : -1.27 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 123 HIS 0.005 0.001 HIS A 67 PHE 0.023 0.002 PHE A 134 TYR 0.056 0.002 TYR A 124 ARG 0.011 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 4.86815 ( 15) link_BETA1-4 : bond 0.00489 ( 3) link_BETA1-4 : angle 3.22458 ( 9) hydrogen bonds : bond 0.03869 ( 416) hydrogen bonds : angle 5.82279 ( 1146) SS BOND : bond 0.00255 ( 22) SS BOND : angle 1.12761 ( 44) covalent geometry : bond 0.00299 (12261) covalent geometry : angle 0.62861 (16660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9563 (tt) cc_final: 0.9317 (tt) REVERT: B 66 HIS cc_start: 0.8632 (t70) cc_final: 0.8420 (t70) REVERT: B 102 LEU cc_start: 0.8857 (tp) cc_final: 0.8656 (tp) REVERT: B 190 SER cc_start: 0.8844 (p) cc_final: 0.8167 (t) REVERT: B 215 GLN cc_start: 0.9593 (tp-100) cc_final: 0.9385 (tp-100) REVERT: B 218 TYR cc_start: 0.9059 (t80) cc_final: 0.8088 (t80) REVERT: B 294 PHE cc_start: 0.8695 (p90) cc_final: 0.8430 (p90) REVERT: C 60 ASP cc_start: 0.8490 (m-30) cc_final: 0.8233 (m-30) REVERT: C 155 ILE cc_start: 0.8210 (pt) cc_final: 0.7651 (mt) REVERT: C 212 MET cc_start: 0.8817 (ptm) cc_final: 0.8014 (pmm) REVERT: C 223 MET cc_start: 0.8404 (pmm) cc_final: 0.7866 (pmm) REVERT: C 280 MET cc_start: 0.9108 (mpp) cc_final: 0.7573 (tpt) REVERT: C 449 MET cc_start: 0.7375 (tmm) cc_final: 0.6993 (tpp) REVERT: C 558 PHE cc_start: 0.8009 (m-10) cc_final: 0.7102 (m-10) REVERT: D 172 LEU cc_start: 0.9358 (mm) cc_final: 0.9067 (mm) REVERT: D 178 ASN cc_start: 0.8172 (t0) cc_final: 0.7827 (t0) REVERT: D 308 PHE cc_start: 0.8279 (m-10) cc_final: 0.7260 (m-10) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2174 time to fit residues: 62.7032 Evaluate side-chains 156 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 59 optimal weight: 0.0060 chunk 146 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 111 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 74 GLN A 138 ASN A 147 GLN A 206 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.109802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083435 restraints weight = 61417.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.086005 restraints weight = 40692.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.087954 restraints weight = 29803.694| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12291 Z= 0.107 Angle : 0.635 11.417 16728 Z= 0.309 Chirality : 0.044 0.329 1874 Planarity : 0.004 0.049 2122 Dihedral : 6.139 58.352 1774 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.07 % Allowed : 5.22 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.57 (0.22), residues: 1468 helix: 0.49 (0.49), residues: 107 sheet: 0.49 (0.21), residues: 605 loop : -1.26 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 123 HIS 0.005 0.001 HIS B 105 PHE 0.017 0.001 PHE A 134 TYR 0.021 0.001 TYR A 124 ARG 0.015 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 5) link_NAG-ASN : angle 4.58520 ( 15) link_BETA1-4 : bond 0.00703 ( 3) link_BETA1-4 : angle 3.14728 ( 9) hydrogen bonds : bond 0.03583 ( 416) hydrogen bonds : angle 5.56802 ( 1146) SS BOND : bond 0.00255 ( 22) SS BOND : angle 0.95930 ( 44) covalent geometry : bond 0.00234 (12261) covalent geometry : angle 0.61470 (16660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9569 (tt) cc_final: 0.9270 (tt) REVERT: A 42 LYS cc_start: 0.9710 (ptmm) cc_final: 0.9505 (ptmm) REVERT: A 209 MET cc_start: 0.9518 (tmm) cc_final: 0.9123 (tpt) REVERT: B 66 HIS cc_start: 0.8627 (t70) cc_final: 0.8423 (t70) REVERT: B 147 MET cc_start: 0.9294 (ptm) cc_final: 0.9090 (ptm) REVERT: B 190 SER cc_start: 0.8839 (p) cc_final: 0.8139 (t) REVERT: B 204 LEU cc_start: 0.9233 (mm) cc_final: 0.8724 (pp) REVERT: B 215 GLN cc_start: 0.9653 (tp-100) cc_final: 0.9432 (tp-100) REVERT: B 216 ASN cc_start: 0.8720 (m-40) cc_final: 0.8230 (m-40) REVERT: B 218 TYR cc_start: 0.8691 (t80) cc_final: 0.8015 (t80) REVERT: B 294 PHE cc_start: 0.8596 (p90) cc_final: 0.8333 (p90) REVERT: C 60 ASP cc_start: 0.8733 (m-30) cc_final: 0.8257 (m-30) REVERT: C 72 ASP cc_start: 0.7635 (p0) cc_final: 0.7197 (p0) REVERT: C 128 LEU cc_start: 0.9140 (pt) cc_final: 0.8468 (tp) REVERT: C 142 LEU cc_start: 0.8930 (mt) cc_final: 0.8729 (mt) REVERT: C 155 ILE cc_start: 0.8212 (pt) cc_final: 0.7653 (mt) REVERT: C 212 MET cc_start: 0.8828 (ptm) cc_final: 0.8007 (pmm) REVERT: C 223 MET cc_start: 0.8370 (pmm) cc_final: 0.7862 (pmm) REVERT: C 280 MET cc_start: 0.9090 (mpp) cc_final: 0.7728 (tpt) REVERT: C 310 MET cc_start: 0.8009 (tmm) cc_final: 0.7768 (tmm) REVERT: C 449 MET cc_start: 0.7592 (tmm) cc_final: 0.7249 (tpp) REVERT: D 172 LEU cc_start: 0.9498 (mm) cc_final: 0.9176 (mm) REVERT: D 308 PHE cc_start: 0.8190 (m-10) cc_final: 0.7199 (m-10) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2123 time to fit residues: 61.9252 Evaluate side-chains 160 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 93 optimal weight: 0.0040 chunk 91 optimal weight: 8.9990 chunk 46 optimal weight: 0.0070 chunk 116 optimal weight: 8.9990 chunk 95 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 138 ASN A 147 GLN A 206 ASN B 91 HIS B 214 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 487 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.110914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084287 restraints weight = 60830.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.086980 restraints weight = 40356.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088864 restraints weight = 29477.033| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12291 Z= 0.102 Angle : 0.627 11.549 16728 Z= 0.304 Chirality : 0.044 0.342 1874 Planarity : 0.005 0.055 2122 Dihedral : 5.853 58.362 1774 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.49 (0.22), residues: 1468 helix: 0.42 (0.49), residues: 109 sheet: 0.55 (0.21), residues: 604 loop : -1.20 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 408 HIS 0.005 0.001 HIS B 105 PHE 0.012 0.001 PHE A 134 TYR 0.011 0.001 TYR A 58 ARG 0.008 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 5) link_NAG-ASN : angle 4.48005 ( 15) link_BETA1-4 : bond 0.00805 ( 3) link_BETA1-4 : angle 3.05426 ( 9) hydrogen bonds : bond 0.03451 ( 416) hydrogen bonds : angle 5.36988 ( 1146) SS BOND : bond 0.00246 ( 22) SS BOND : angle 1.18536 ( 44) covalent geometry : bond 0.00224 (12261) covalent geometry : angle 0.60643 (16660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9553 (tt) cc_final: 0.9251 (tt) REVERT: A 159 ILE cc_start: 0.9063 (tp) cc_final: 0.8791 (tp) REVERT: B 23 MET cc_start: 0.7401 (mmt) cc_final: 0.7003 (mmt) REVERT: B 24 TRP cc_start: 0.7656 (p90) cc_final: 0.6141 (p90) REVERT: B 32 VAL cc_start: 0.7709 (m) cc_final: 0.7400 (m) REVERT: B 190 SER cc_start: 0.8838 (p) cc_final: 0.8126 (t) REVERT: B 204 LEU cc_start: 0.9233 (mm) cc_final: 0.8707 (pp) REVERT: B 215 GLN cc_start: 0.9666 (tp-100) cc_final: 0.9451 (tp-100) REVERT: B 216 ASN cc_start: 0.8739 (m-40) cc_final: 0.8231 (m-40) REVERT: B 218 TYR cc_start: 0.8673 (t80) cc_final: 0.8142 (t80) REVERT: B 294 PHE cc_start: 0.8514 (p90) cc_final: 0.8265 (p90) REVERT: C 60 ASP cc_start: 0.8629 (m-30) cc_final: 0.8143 (m-30) REVERT: C 155 ILE cc_start: 0.8217 (pt) cc_final: 0.7644 (mt) REVERT: C 212 MET cc_start: 0.8839 (ptm) cc_final: 0.8001 (pmm) REVERT: C 280 MET cc_start: 0.9053 (mpp) cc_final: 0.7690 (tpt) REVERT: C 449 MET cc_start: 0.7569 (tmm) cc_final: 0.7250 (tpp) REVERT: C 536 MET cc_start: 0.8392 (pmm) cc_final: 0.7488 (tpt) REVERT: D 172 LEU cc_start: 0.9466 (mm) cc_final: 0.9087 (mm) REVERT: D 308 PHE cc_start: 0.8123 (m-10) cc_final: 0.7100 (m-10) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2139 time to fit residues: 63.9673 Evaluate side-chains 164 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 0.0980 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 74 GLN A 110 GLN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.099864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074236 restraints weight = 65574.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076389 restraints weight = 44633.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078004 restraints weight = 33568.962| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12291 Z= 0.298 Angle : 0.842 15.452 16728 Z= 0.418 Chirality : 0.047 0.325 1874 Planarity : 0.006 0.054 2122 Dihedral : 6.641 59.205 1774 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.20 (0.21), residues: 1468 helix: -0.72 (0.44), residues: 110 sheet: -0.01 (0.21), residues: 586 loop : -1.45 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 112 HIS 0.013 0.002 HIS A 67 PHE 0.030 0.003 PHE A 198 TYR 0.029 0.003 TYR A 185 ARG 0.016 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 5) link_NAG-ASN : angle 5.27805 ( 15) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 3.14794 ( 9) hydrogen bonds : bond 0.04927 ( 416) hydrogen bonds : angle 6.19464 ( 1146) SS BOND : bond 0.00831 ( 22) SS BOND : angle 1.43084 ( 44) covalent geometry : bond 0.00622 (12261) covalent geometry : angle 0.82181 (16660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.9610 (mp0) cc_final: 0.9399 (pm20) REVERT: A 110 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5764 (pp30) REVERT: A 189 MET cc_start: 0.8476 (mmp) cc_final: 0.8227 (mmm) REVERT: B 136 ARG cc_start: 0.7803 (ttt-90) cc_final: 0.7182 (ttt-90) REVERT: B 190 SER cc_start: 0.9068 (p) cc_final: 0.8427 (t) REVERT: B 208 LEU cc_start: 0.8420 (mm) cc_final: 0.8195 (mm) REVERT: B 218 TYR cc_start: 0.8836 (t80) cc_final: 0.8578 (t80) REVERT: C 60 ASP cc_start: 0.8757 (m-30) cc_final: 0.8442 (m-30) REVERT: C 155 ILE cc_start: 0.8552 (pt) cc_final: 0.8150 (mt) REVERT: C 212 MET cc_start: 0.8939 (ptm) cc_final: 0.8083 (pmm) REVERT: C 449 MET cc_start: 0.7749 (tmm) cc_final: 0.7226 (tpp) REVERT: C 472 HIS cc_start: 0.8368 (m90) cc_final: 0.8076 (m-70) REVERT: C 558 PHE cc_start: 0.7853 (m-80) cc_final: 0.7459 (m-80) REVERT: D 308 PHE cc_start: 0.8083 (m-10) cc_final: 0.7197 (m-10) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2276 time to fit residues: 59.9503 Evaluate side-chains 141 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 112 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 6 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.104084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077813 restraints weight = 60186.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080274 restraints weight = 39912.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082109 restraints weight = 29298.844| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12291 Z= 0.140 Angle : 0.689 11.294 16728 Z= 0.337 Chirality : 0.046 0.355 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.358 59.782 1774 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.92 (0.21), residues: 1468 helix: -0.22 (0.47), residues: 109 sheet: 0.15 (0.21), residues: 594 loop : -1.29 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 112 HIS 0.010 0.001 HIS B 105 PHE 0.021 0.002 PHE B 270 TYR 0.016 0.001 TYR A 185 ARG 0.013 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 5) link_NAG-ASN : angle 5.05319 ( 15) link_BETA1-4 : bond 0.00603 ( 3) link_BETA1-4 : angle 3.07789 ( 9) hydrogen bonds : bond 0.03803 ( 416) hydrogen bonds : angle 5.74821 ( 1146) SS BOND : bond 0.00336 ( 22) SS BOND : angle 1.54084 ( 44) covalent geometry : bond 0.00309 (12261) covalent geometry : angle 0.66498 (16660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9573 (tt) cc_final: 0.9348 (tt) REVERT: A 85 GLU cc_start: 0.9603 (mp0) cc_final: 0.9394 (pm20) REVERT: A 189 MET cc_start: 0.8246 (mmp) cc_final: 0.8028 (mmm) REVERT: B 136 ARG cc_start: 0.8010 (ttt-90) cc_final: 0.7503 (ttt-90) REVERT: B 190 SER cc_start: 0.8832 (p) cc_final: 0.8092 (t) REVERT: B 218 TYR cc_start: 0.8894 (t80) cc_final: 0.8402 (t80) REVERT: C 60 ASP cc_start: 0.8479 (m-30) cc_final: 0.8115 (m-30) REVERT: C 128 LEU cc_start: 0.9362 (pt) cc_final: 0.8947 (mm) REVERT: C 155 ILE cc_start: 0.8472 (pt) cc_final: 0.8006 (mt) REVERT: C 212 MET cc_start: 0.8961 (ptm) cc_final: 0.8104 (pmm) REVERT: C 280 MET cc_start: 0.9082 (mpp) cc_final: 0.7667 (tpt) REVERT: C 310 MET cc_start: 0.8090 (tmm) cc_final: 0.7885 (tmm) REVERT: C 449 MET cc_start: 0.7602 (tmm) cc_final: 0.6991 (tpp) REVERT: C 472 HIS cc_start: 0.8001 (m90) cc_final: 0.7727 (m-70) REVERT: C 558 PHE cc_start: 0.7973 (m-80) cc_final: 0.7688 (m-80) REVERT: D 172 LEU cc_start: 0.9448 (mm) cc_final: 0.9171 (mm) REVERT: D 199 LEU cc_start: 0.8933 (mm) cc_final: 0.8429 (tp) REVERT: D 308 PHE cc_start: 0.8137 (m-10) cc_final: 0.7096 (m-10) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2291 time to fit residues: 61.9272 Evaluate side-chains 150 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 105 optimal weight: 8.9990 chunk 3 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 92 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 21 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 overall best weight: 0.7074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 111 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.106012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079650 restraints weight = 60603.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082210 restraints weight = 39631.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.083973 restraints weight = 28898.741| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12291 Z= 0.116 Angle : 0.687 12.553 16728 Z= 0.332 Chirality : 0.045 0.338 1874 Planarity : 0.005 0.052 2122 Dihedral : 6.194 58.524 1774 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.70 (0.21), residues: 1468 helix: 0.19 (0.48), residues: 109 sheet: 0.37 (0.21), residues: 579 loop : -1.23 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 145 HIS 0.013 0.001 HIS B 105 PHE 0.012 0.001 PHE D 303 TYR 0.012 0.001 TYR A 124 ARG 0.010 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 5) link_NAG-ASN : angle 4.74416 ( 15) link_BETA1-4 : bond 0.00644 ( 3) link_BETA1-4 : angle 3.02268 ( 9) hydrogen bonds : bond 0.03609 ( 416) hydrogen bonds : angle 5.50494 ( 1146) SS BOND : bond 0.00283 ( 22) SS BOND : angle 1.94102 ( 44) covalent geometry : bond 0.00264 (12261) covalent geometry : angle 0.66274 (16660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9528 (tt) cc_final: 0.9289 (tt) REVERT: A 85 GLU cc_start: 0.9611 (mp0) cc_final: 0.9239 (pm20) REVERT: A 189 MET cc_start: 0.8217 (mmp) cc_final: 0.7992 (mmm) REVERT: B 23 MET cc_start: 0.7109 (mmt) cc_final: 0.6025 (mmt) REVERT: B 36 ASP cc_start: 0.7905 (p0) cc_final: 0.7594 (p0) REVERT: B 66 HIS cc_start: 0.8540 (t70) cc_final: 0.8331 (t70) REVERT: B 88 TYR cc_start: 0.8054 (m-80) cc_final: 0.7733 (m-80) REVERT: B 102 LEU cc_start: 0.9338 (tp) cc_final: 0.8985 (tp) REVERT: B 136 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7456 (ttt-90) REVERT: B 190 SER cc_start: 0.8756 (p) cc_final: 0.7977 (t) REVERT: B 204 LEU cc_start: 0.9069 (mp) cc_final: 0.8742 (pt) REVERT: B 257 ASP cc_start: 0.9159 (p0) cc_final: 0.8955 (p0) REVERT: B 294 PHE cc_start: 0.8627 (p90) cc_final: 0.8387 (p90) REVERT: C 60 ASP cc_start: 0.8505 (m-30) cc_final: 0.8122 (m-30) REVERT: C 128 LEU cc_start: 0.9349 (pt) cc_final: 0.8948 (mm) REVERT: C 155 ILE cc_start: 0.8342 (pt) cc_final: 0.7871 (mt) REVERT: C 212 MET cc_start: 0.9031 (ptm) cc_final: 0.8201 (pmm) REVERT: C 280 MET cc_start: 0.9023 (mpp) cc_final: 0.7643 (tpt) REVERT: C 449 MET cc_start: 0.7658 (tmm) cc_final: 0.7084 (tpp) REVERT: C 472 HIS cc_start: 0.8159 (m90) cc_final: 0.7875 (m-70) REVERT: C 558 PHE cc_start: 0.7894 (m-80) cc_final: 0.7624 (m-80) REVERT: D 172 LEU cc_start: 0.9485 (mm) cc_final: 0.9132 (mm) REVERT: D 308 PHE cc_start: 0.8061 (m-10) cc_final: 0.6965 (m-10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2214 time to fit residues: 62.8989 Evaluate side-chains 147 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 147 GLN A 206 ASN B 91 HIS B 109 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.106691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080155 restraints weight = 59204.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082768 restraints weight = 39145.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084619 restraints weight = 28570.931| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12291 Z= 0.110 Angle : 0.671 11.419 16728 Z= 0.324 Chirality : 0.044 0.335 1874 Planarity : 0.004 0.052 2122 Dihedral : 6.059 57.537 1774 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.61 (0.22), residues: 1468 helix: 0.40 (0.50), residues: 109 sheet: 0.41 (0.21), residues: 585 loop : -1.18 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 109 HIS 0.007 0.001 HIS B 105 PHE 0.012 0.001 PHE C 122 TYR 0.012 0.001 TYR B 218 ARG 0.012 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 5) link_NAG-ASN : angle 4.59578 ( 15) link_BETA1-4 : bond 0.00662 ( 3) link_BETA1-4 : angle 2.97905 ( 9) hydrogen bonds : bond 0.03559 ( 416) hydrogen bonds : angle 5.39684 ( 1146) SS BOND : bond 0.00251 ( 22) SS BOND : angle 1.64389 ( 44) covalent geometry : bond 0.00249 (12261) covalent geometry : angle 0.64923 (16660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9541 (tt) cc_final: 0.9220 (tt) REVERT: A 66 ASP cc_start: 0.8117 (m-30) cc_final: 0.7887 (m-30) REVERT: A 85 GLU cc_start: 0.9613 (mp0) cc_final: 0.9230 (pm20) REVERT: A 129 MET cc_start: 0.9638 (mpp) cc_final: 0.9407 (mpp) REVERT: A 189 MET cc_start: 0.8272 (mmp) cc_final: 0.8044 (mmm) REVERT: B 102 LEU cc_start: 0.9382 (tp) cc_final: 0.9101 (tp) REVERT: B 108 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8777 (mm-30) REVERT: B 136 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7572 (ttt-90) REVERT: B 204 LEU cc_start: 0.9101 (mp) cc_final: 0.8767 (pt) REVERT: B 241 MET cc_start: 0.3998 (tmm) cc_final: 0.2829 (ttt) REVERT: B 294 PHE cc_start: 0.8487 (p90) cc_final: 0.8223 (p90) REVERT: C 60 ASP cc_start: 0.8480 (m-30) cc_final: 0.8232 (m-30) REVERT: C 128 LEU cc_start: 0.9353 (pt) cc_final: 0.8927 (mm) REVERT: C 155 ILE cc_start: 0.8295 (pt) cc_final: 0.7857 (mt) REVERT: C 212 MET cc_start: 0.9042 (ptm) cc_final: 0.8223 (pmm) REVERT: C 280 MET cc_start: 0.9012 (mpp) cc_final: 0.7630 (tpt) REVERT: C 449 MET cc_start: 0.7757 (tmm) cc_final: 0.7360 (tpp) REVERT: C 472 HIS cc_start: 0.8163 (m90) cc_final: 0.7881 (m-70) REVERT: C 558 PHE cc_start: 0.7855 (m-80) cc_final: 0.7572 (m-80) REVERT: D 172 LEU cc_start: 0.9478 (mm) cc_final: 0.9148 (mm) REVERT: D 308 PHE cc_start: 0.8041 (m-10) cc_final: 0.6936 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2300 time to fit residues: 65.2419 Evaluate side-chains 151 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 75 optimal weight: 0.0870 chunk 110 optimal weight: 0.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.107656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081767 restraints weight = 60721.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084315 restraints weight = 40195.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086228 restraints weight = 29413.540| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12291 Z= 0.105 Angle : 0.661 12.090 16728 Z= 0.319 Chirality : 0.044 0.338 1874 Planarity : 0.004 0.053 2122 Dihedral : 5.962 57.937 1774 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.48 (0.22), residues: 1468 helix: 0.56 (0.50), residues: 107 sheet: 0.54 (0.21), residues: 578 loop : -1.13 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 109 HIS 0.008 0.001 HIS B 105 PHE 0.013 0.001 PHE D 303 TYR 0.031 0.001 TYR B 187 ARG 0.010 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 5) link_NAG-ASN : angle 4.66245 ( 15) link_BETA1-4 : bond 0.00725 ( 3) link_BETA1-4 : angle 3.01161 ( 9) hydrogen bonds : bond 0.03503 ( 416) hydrogen bonds : angle 5.34201 ( 1146) SS BOND : bond 0.00230 ( 22) SS BOND : angle 1.46076 ( 44) covalent geometry : bond 0.00237 (12261) covalent geometry : angle 0.63947 (16660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9540 (tt) cc_final: 0.9233 (tt) REVERT: A 66 ASP cc_start: 0.8067 (m-30) cc_final: 0.7832 (m-30) REVERT: A 85 GLU cc_start: 0.9624 (mp0) cc_final: 0.9234 (pm20) REVERT: A 159 ILE cc_start: 0.9052 (tp) cc_final: 0.8532 (tp) REVERT: B 36 ASP cc_start: 0.8073 (p0) cc_final: 0.7835 (p0) REVERT: B 108 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8937 (mm-30) REVERT: B 136 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7488 (ttt-90) REVERT: B 204 LEU cc_start: 0.9095 (mp) cc_final: 0.8759 (pt) REVERT: B 241 MET cc_start: 0.3506 (tmm) cc_final: 0.2145 (ttt) REVERT: B 257 ASP cc_start: 0.9141 (p0) cc_final: 0.8940 (p0) REVERT: B 294 PHE cc_start: 0.8530 (p90) cc_final: 0.8223 (p90) REVERT: C 60 ASP cc_start: 0.8525 (m-30) cc_final: 0.8222 (m-30) REVERT: C 128 LEU cc_start: 0.9330 (pt) cc_final: 0.8900 (mm) REVERT: C 155 ILE cc_start: 0.8296 (pt) cc_final: 0.7813 (mt) REVERT: C 157 VAL cc_start: 0.8948 (p) cc_final: 0.8737 (p) REVERT: C 212 MET cc_start: 0.9044 (ptm) cc_final: 0.8283 (pmm) REVERT: C 280 MET cc_start: 0.9009 (mpp) cc_final: 0.7650 (tpt) REVERT: C 558 PHE cc_start: 0.7819 (m-80) cc_final: 0.7555 (m-80) REVERT: D 172 LEU cc_start: 0.9454 (mm) cc_final: 0.9105 (mm) REVERT: D 308 PHE cc_start: 0.8039 (m-10) cc_final: 0.6956 (m-10) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2091 time to fit residues: 61.5518 Evaluate side-chains 153 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 25 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 81 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN A 206 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.106665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080512 restraints weight = 59908.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.083049 restraints weight = 39848.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084832 restraints weight = 29108.261| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12291 Z= 0.110 Angle : 0.655 11.661 16728 Z= 0.317 Chirality : 0.044 0.355 1874 Planarity : 0.004 0.053 2122 Dihedral : 5.887 57.555 1774 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.46 (0.22), residues: 1468 helix: 0.63 (0.50), residues: 107 sheet: 0.52 (0.21), residues: 582 loop : -1.11 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 112 HIS 0.012 0.001 HIS B 105 PHE 0.012 0.001 PHE D 303 TYR 0.014 0.001 TYR B 187 ARG 0.008 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 5) link_NAG-ASN : angle 4.64907 ( 15) link_BETA1-4 : bond 0.00637 ( 3) link_BETA1-4 : angle 2.94238 ( 9) hydrogen bonds : bond 0.03535 ( 416) hydrogen bonds : angle 5.38335 ( 1146) SS BOND : bond 0.00214 ( 22) SS BOND : angle 1.42298 ( 44) covalent geometry : bond 0.00246 (12261) covalent geometry : angle 0.63385 (16660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4509.38 seconds wall clock time: 79 minutes 33.40 seconds (4773.40 seconds total)