Starting phenix.real_space_refine on Wed Jul 30 07:24:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oe0_16821/07_2025/8oe0_16821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oe0_16821/07_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_16821/07_2025/8oe0_16821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oe0_16821/07_2025/8oe0_16821.map" model { file = "/net/cci-nas-00/data/ceres_data/8oe0_16821/07_2025/8oe0_16821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oe0_16821/07_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-5711/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: 6.93, per 1000 atoms: 0.58 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 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: 1.50 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: 4.15 Time building geometry restraints manager: 3.26 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 28.680 Find NCS groups from input model: 0.150 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- 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 : 1.313 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: 0.2616 time to fit residues: 91.5345 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 : 1.288 ------------------------------------------------------------------------------- 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 = 0.108509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.082470 restraints weight = 62508.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.084920 restraints weight = 42149.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086752 restraints weight = 31225.597| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 1.938 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: 0.9606 (tt) cc_final: 0.9321 (tt) REVERT: A 42 LYS cc_start: 0.9716 (ptmm) cc_final: 0.9502 (ptmm) REVERT: A 159 ILE cc_start: 0.9086 (tp) cc_final: 0.8549 (tp) REVERT: A 163 MET cc_start: 0.8902 (mmt) cc_final: 0.8680 (mmm) REVERT: B 66 HIS cc_start: 0.8581 (t70) cc_final: 0.8380 (t70) REVERT: B 136 ARG cc_start: 0.7963 (ttt-90) cc_final: 0.7404 (tmt-80) REVERT: B 172 LEU cc_start: 0.9671 (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: 0.9611 (tp-100) cc_final: 0.9364 (tp-100) REVERT: B 218 TYR cc_start: 0.9089 (t80) cc_final: 0.8262 (t80) REVERT: B 294 PHE cc_start: 0.8679 (p90) cc_final: 0.8456 (p90) REVERT: C 50 ASN cc_start: 0.9027 (m-40) cc_final: 0.8755 (m110) REVERT: C 60 ASP cc_start: 0.8622 (m-30) cc_final: 0.8301 (m-30) REVERT: C 155 ILE cc_start: 0.8255 (pt) cc_final: 0.7689 (mt) REVERT: C 212 MET cc_start: 0.8765 (ptm) cc_final: 0.7985 (pmm) REVERT: C 223 MET cc_start: 0.8320 (pmm) cc_final: 0.7868 (pmm) REVERT: D 172 LEU cc_start: 0.9446 (mm) cc_final: 0.9094 (mm) REVERT: D 308 PHE cc_start: 0.8431 (m-10) cc_final: 0.7513 (m-10) REVERT: D 408 TRP cc_start: 0.8480 (m-90) cc_final: 0.7993 (m-90) outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.2357 time to fit residues: 66.1000 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 : 1.438 ------------------------------------------------------------------------------- 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: 10.0000 chunk 24 optimal weight: 0.0050 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 540 GLN D 309 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 = 0.4042 r_free = 0.4042 target = 0.107401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081335 restraints weight = 63366.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.083820 restraints weight = 42308.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085642 restraints weight = 31124.244| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12291 Z= 0.149 Angle : 0.658 11.874 16728 Z= 0.325 Chirality : 0.044 0.339 1874 Planarity : 0.005 0.070 2122 Dihedral : 6.541 57.823 1774 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % 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: -0.71 (0.21), residues: 1468 helix: 0.34 (0.49), residues: 107 sheet: 0.35 (0.21), residues: 599 loop : -1.29 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 123 HIS 0.005 0.001 HIS A 67 PHE 0.023 0.002 PHE A 134 TYR 0.048 0.002 TYR A 124 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 4.86050 ( 15) link_BETA1-4 : bond 0.00370 ( 3) link_BETA1-4 : angle 3.28432 ( 9) hydrogen bonds : bond 0.03932 ( 416) hydrogen bonds : angle 5.84483 ( 1146) SS BOND : bond 0.00218 ( 22) SS BOND : angle 1.15935 ( 44) covalent geometry : bond 0.00316 (12261) covalent geometry : angle 0.63565 (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 195 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.544 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: 0.9587 (tt) cc_final: 0.9353 (tt) REVERT: B 66 HIS cc_start: 0.8650 (t70) cc_final: 0.8430 (t70) REVERT: B 102 LEU cc_start: 0.8864 (tp) cc_final: 0.8649 (tp) REVERT: B 190 SER cc_start: 0.8852 (p) cc_final: 0.8181 (t) REVERT: B 215 GLN cc_start: 0.9598 (tp-100) cc_final: 0.9394 (tp-100) REVERT: B 218 TYR cc_start: 0.9073 (t80) cc_final: 0.8089 (t80) REVERT: B 294 PHE cc_start: 0.8630 (p90) cc_final: 0.8390 (p90) REVERT: C 60 ASP cc_start: 0.8473 (m-30) cc_final: 0.8149 (m-30) REVERT: C 155 ILE cc_start: 0.8218 (pt) cc_final: 0.7663 (mt) REVERT: C 212 MET cc_start: 0.8824 (ptm) cc_final: 0.7705 (pmm) REVERT: C 223 MET cc_start: 0.8407 (pmm) cc_final: 0.7874 (pmm) REVERT: C 280 MET cc_start: 0.9127 (mpp) cc_final: 0.7581 (tpt) REVERT: C 449 MET cc_start: 0.7408 (tmm) cc_final: 0.7024 (tpp) REVERT: C 558 PHE cc_start: 0.8010 (m-10) cc_final: 0.7109 (m-10) REVERT: D 172 LEU cc_start: 0.9362 (mm) cc_final: 0.9074 (mm) REVERT: D 178 ASN cc_start: 0.8147 (t0) cc_final: 0.7781 (t0) REVERT: D 308 PHE cc_start: 0.8264 (m-10) cc_final: 0.7261 (m-10) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.2814 time to fit residues: 80.1556 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 : 1.623 ------------------------------------------------------------------------------- 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: 0.8980 chunk 146 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.106782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.080750 restraints weight = 63305.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.083199 restraints weight = 42694.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.084979 restraints weight = 31643.735| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12291 Z= 0.136 Angle : 0.650 11.294 16728 Z= 0.319 Chirality : 0.043 0.329 1874 Planarity : 0.005 0.048 2122 Dihedral : 6.309 59.310 1774 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -0.74 (0.21), residues: 1468 helix: -0.02 (0.46), residues: 113 sheet: 0.34 (0.21), residues: 600 loop : -1.27 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 408 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.002 PHE A 198 TYR 0.019 0.001 TYR A 124 ARG 0.015 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 5) link_NAG-ASN : angle 4.74171 ( 15) link_BETA1-4 : bond 0.00564 ( 3) link_BETA1-4 : angle 3.10326 ( 9) hydrogen bonds : bond 0.03776 ( 416) hydrogen bonds : angle 5.72484 ( 1146) SS BOND : bond 0.00276 ( 22) SS BOND : angle 0.99465 ( 44) covalent geometry : bond 0.00296 (12261) covalent geometry : angle 0.62967 (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 186 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.248 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: 0.9558 (tt) cc_final: 0.9226 (tt) REVERT: A 42 LYS cc_start: 0.9712 (ptmm) cc_final: 0.9464 (ptmm) REVERT: A 209 MET cc_start: 0.9565 (tmm) cc_final: 0.9148 (tpt) REVERT: B 136 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7647 (ttt-90) REVERT: B 190 SER cc_start: 0.8826 (p) cc_final: 0.8367 (p) REVERT: B 218 TYR cc_start: 0.8745 (t80) cc_final: 0.8081 (t80) REVERT: B 294 PHE cc_start: 0.8650 (p90) cc_final: 0.8384 (p90) REVERT: C 60 ASP cc_start: 0.8571 (m-30) cc_final: 0.8005 (m-30) REVERT: C 142 LEU cc_start: 0.8918 (mt) cc_final: 0.8695 (mt) REVERT: C 155 ILE cc_start: 0.8298 (pt) cc_final: 0.7821 (mt) REVERT: C 212 MET cc_start: 0.8856 (ptm) cc_final: 0.7723 (pmm) REVERT: C 223 MET cc_start: 0.8389 (pmm) cc_final: 0.7854 (pmm) REVERT: C 280 MET cc_start: 0.9155 (mpp) cc_final: 0.7739 (tpt) REVERT: C 310 MET cc_start: 0.8067 (tmm) cc_final: 0.7783 (tmm) REVERT: C 449 MET cc_start: 0.7465 (tmm) cc_final: 0.7095 (tpp) REVERT: D 172 LEU cc_start: 0.9420 (mm) cc_final: 0.9095 (mm) REVERT: D 308 PHE cc_start: 0.8233 (m-10) cc_final: 0.7239 (m-10) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2647 time to fit residues: 73.8178 Evaluate side-chains 158 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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: 20.0000 chunk 91 optimal weight: 0.0970 chunk 46 optimal weight: 0.0670 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 67 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.109818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082906 restraints weight = 57315.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085437 restraints weight = 38503.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087375 restraints weight = 28471.814| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2676 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= 0.104 Angle : 0.639 11.423 16728 Z= 0.309 Chirality : 0.045 0.336 1874 Planarity : 0.005 0.056 2122 Dihedral : 5.996 58.336 1774 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: -0.56 (0.22), residues: 1468 helix: 0.14 (0.47), residues: 115 sheet: 0.51 (0.21), residues: 606 loop : -1.22 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 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 0.015 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 5) link_NAG-ASN : angle 4.51793 ( 15) link_BETA1-4 : bond 0.00674 ( 3) link_BETA1-4 : angle 3.07329 ( 9) hydrogen bonds : bond 0.03482 ( 416) hydrogen bonds : angle 5.43690 ( 1146) SS BOND : bond 0.00246 ( 22) SS BOND : angle 1.24255 ( 44) covalent geometry : bond 0.00227 (12261) covalent geometry : angle 0.61801 (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 207 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.827 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: 0.9562 (tt) cc_final: 0.9287 (tt) REVERT: A 69 ASP cc_start: 0.9109 (p0) cc_final: 0.8861 (p0) REVERT: B 66 HIS cc_start: 0.8516 (t70) cc_final: 0.8198 (t70) REVERT: B 136 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7460 (ttt-90) REVERT: B 190 SER cc_start: 0.8812 (p) cc_final: 0.7867 (t) REVERT: B 204 LEU cc_start: 0.9038 (mp) cc_final: 0.8580 (pp) REVERT: B 218 TYR cc_start: 0.8681 (t80) cc_final: 0.8024 (t80) REVERT: B 294 PHE cc_start: 0.8567 (p90) cc_final: 0.8323 (p90) REVERT: C 60 ASP cc_start: 0.8592 (m-30) cc_final: 0.8107 (m-30) REVERT: C 152 LEU cc_start: 0.8591 (tp) cc_final: 0.8382 (tp) REVERT: C 155 ILE cc_start: 0.8199 (pt) cc_final: 0.7740 (mt) REVERT: C 212 MET cc_start: 0.8869 (ptm) cc_final: 0.7715 (pmm) REVERT: C 280 MET cc_start: 0.9080 (mpp) cc_final: 0.7685 (tpt) REVERT: C 449 MET cc_start: 0.7356 (tmm) cc_final: 0.6990 (tpp) REVERT: C 536 MET cc_start: 0.8303 (pmm) cc_final: 0.7427 (tpt) REVERT: D 172 LEU cc_start: 0.9477 (mm) cc_final: 0.9121 (mm) REVERT: D 308 PHE cc_start: 0.8109 (m-10) cc_final: 0.7306 (m-10) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3686 time to fit residues: 110.1522 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 : 1.546 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 chunk 130 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 overall best weight: 2.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 110 GLN A 138 ASN 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 215 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.103728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.077760 restraints weight = 61537.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.080089 restraints weight = 41326.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081871 restraints weight = 30688.597| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12291 Z= 0.188 Angle : 0.709 11.057 16728 Z= 0.348 Chirality : 0.044 0.345 1874 Planarity : 0.005 0.057 2122 Dihedral : 6.270 56.841 1774 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.49 % 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: -0.84 (0.21), residues: 1468 helix: -0.28 (0.46), residues: 110 sheet: 0.28 (0.21), residues: 600 loop : -1.30 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 112 HIS 0.011 0.002 HIS B 105 PHE 0.019 0.002 PHE A 198 TYR 0.018 0.002 TYR A 185 ARG 0.010 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 5) link_NAG-ASN : angle 5.11147 ( 15) link_BETA1-4 : bond 0.00588 ( 3) link_BETA1-4 : angle 3.13217 ( 9) hydrogen bonds : bond 0.04048 ( 416) hydrogen bonds : angle 5.71202 ( 1146) SS BOND : bond 0.00528 ( 22) SS BOND : angle 1.24991 ( 44) covalent geometry : bond 0.00400 (12261) covalent geometry : angle 0.68648 (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 187 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.297 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: 0.9618 (tt) cc_final: 0.9407 (tt) REVERT: A 110 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.5503 (pp30) REVERT: A 155 MET cc_start: 0.9066 (pmm) cc_final: 0.8845 (pmm) REVERT: B 23 MET cc_start: 0.7069 (mmt) cc_final: 0.5714 (mmm) REVERT: B 136 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7467 (ttt-90) REVERT: B 190 SER cc_start: 0.8860 (p) cc_final: 0.8117 (t) REVERT: B 218 TYR cc_start: 0.8831 (t80) cc_final: 0.8177 (t80) REVERT: B 294 PHE cc_start: 0.8748 (p90) cc_final: 0.8489 (p90) REVERT: C 60 ASP cc_start: 0.8761 (m-30) cc_final: 0.8287 (m-30) REVERT: C 155 ILE cc_start: 0.8367 (pt) cc_final: 0.7847 (mt) REVERT: C 212 MET cc_start: 0.8886 (ptm) cc_final: 0.7709 (pmm) REVERT: C 223 MET cc_start: 0.8426 (pmm) cc_final: 0.7903 (pmm) REVERT: C 310 MET cc_start: 0.8101 (tmm) cc_final: 0.7860 (tmm) REVERT: C 449 MET cc_start: 0.7634 (tmm) cc_final: 0.7164 (tpp) REVERT: C 472 HIS cc_start: 0.8223 (m90) cc_final: 0.7935 (m-70) REVERT: C 536 MET cc_start: 0.8356 (pmm) cc_final: 0.7503 (tpt) REVERT: D 172 LEU cc_start: 0.9491 (mm) cc_final: 0.9187 (mm) REVERT: D 308 PHE cc_start: 0.8251 (m-10) cc_final: 0.7267 (m-10) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2228 time to fit residues: 61.7634 Evaluate side-chains 149 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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: 0.7980 chunk 135 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 133 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** 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 = 0.4052 r_free = 0.4052 target = 0.107327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080925 restraints weight = 60264.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083342 restraints weight = 40504.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085218 restraints weight = 30184.237| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12291 Z= 0.114 Angle : 0.664 13.221 16728 Z= 0.320 Chirality : 0.045 0.371 1874 Planarity : 0.004 0.053 2122 Dihedral : 6.099 59.703 1774 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.59 (0.22), residues: 1468 helix: 0.29 (0.48), residues: 109 sheet: 0.44 (0.21), residues: 596 loop : -1.18 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 123 HIS 0.015 0.001 HIS B 105 PHE 0.013 0.001 PHE C 122 TYR 0.010 0.001 TYR A 185 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 5) link_NAG-ASN : angle 4.71518 ( 15) link_BETA1-4 : bond 0.00641 ( 3) link_BETA1-4 : angle 3.18630 ( 9) hydrogen bonds : bond 0.03541 ( 416) hydrogen bonds : angle 5.38879 ( 1146) SS BOND : bond 0.00294 ( 22) SS BOND : angle 1.37085 ( 44) covalent geometry : bond 0.00261 (12261) covalent geometry : angle 0.64221 (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 195 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.406 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 41 LEU cc_start: 0.9544 (tt) cc_final: 0.9308 (tt) REVERT: B 23 MET cc_start: 0.7111 (mmt) cc_final: 0.6169 (mmt) REVERT: B 66 HIS cc_start: 0.8651 (t70) cc_final: 0.8397 (t70) REVERT: B 102 LEU cc_start: 0.9391 (tp) cc_final: 0.9040 (tp) REVERT: B 136 ARG cc_start: 0.7937 (ttt-90) cc_final: 0.7484 (ttt-90) REVERT: B 190 SER cc_start: 0.8749 (p) cc_final: 0.7877 (t) REVERT: B 204 LEU cc_start: 0.9104 (mp) cc_final: 0.8685 (pp) REVERT: B 294 PHE cc_start: 0.8648 (p90) cc_final: 0.8405 (p90) REVERT: C 60 ASP cc_start: 0.8399 (m-30) cc_final: 0.8089 (m-30) REVERT: C 155 ILE cc_start: 0.8298 (pt) cc_final: 0.7837 (mt) REVERT: C 212 MET cc_start: 0.9028 (ptm) cc_final: 0.7988 (pmm) REVERT: C 449 MET cc_start: 0.7636 (tmm) cc_final: 0.7226 (tpp) REVERT: C 472 HIS cc_start: 0.8216 (m90) cc_final: 0.7911 (m-70) REVERT: C 536 MET cc_start: 0.8297 (pmm) cc_final: 0.7283 (tpt) REVERT: D 172 LEU cc_start: 0.9489 (mm) cc_final: 0.9142 (mm) REVERT: D 308 PHE cc_start: 0.8097 (m-10) cc_final: 0.7279 (m-10) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2560 time to fit residues: 74.5214 Evaluate side-chains 152 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 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 = 0.4066 r_free = 0.4066 target = 0.107994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081119 restraints weight = 59359.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.083684 restraints weight = 39470.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085650 restraints weight = 29147.152| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12291 Z= 0.105 Angle : 0.663 11.764 16728 Z= 0.319 Chirality : 0.045 0.345 1874 Planarity : 0.004 0.053 2122 Dihedral : 6.046 59.451 1774 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -0.43 (0.22), residues: 1468 helix: 0.61 (0.51), residues: 109 sheet: 0.65 (0.21), residues: 578 loop : -1.18 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 109 HIS 0.009 0.001 HIS B 105 PHE 0.012 0.001 PHE C 122 TYR 0.012 0.001 TYR B 218 ARG 0.017 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 5.01678 ( 15) link_BETA1-4 : bond 0.00706 ( 3) link_BETA1-4 : angle 3.06992 ( 9) hydrogen bonds : bond 0.03530 ( 416) hydrogen bonds : angle 5.34162 ( 1146) SS BOND : bond 0.00316 ( 22) SS BOND : angle 1.85305 ( 44) covalent geometry : bond 0.00237 (12261) covalent geometry : angle 0.63565 (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 196 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.281 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: 0.9565 (tt) cc_final: 0.9362 (tt) REVERT: A 85 GLU cc_start: 0.9536 (mp0) cc_final: 0.9151 (pm20) REVERT: B 23 MET cc_start: 0.7010 (mmt) cc_final: 0.6411 (mpp) REVERT: B 66 HIS cc_start: 0.8665 (t70) cc_final: 0.8426 (t70) REVERT: B 102 LEU cc_start: 0.9315 (tp) cc_final: 0.8931 (tp) REVERT: B 125 PHE cc_start: 0.8659 (m-10) cc_final: 0.8453 (m-80) REVERT: B 136 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.7442 (ttt-90) REVERT: B 137 PHE cc_start: 0.9038 (p90) cc_final: 0.8808 (p90) REVERT: B 190 SER cc_start: 0.8793 (p) cc_final: 0.7992 (t) REVERT: B 204 LEU cc_start: 0.9071 (mp) cc_final: 0.8655 (pp) REVERT: B 294 PHE cc_start: 0.8604 (p90) cc_final: 0.8334 (p90) REVERT: C 60 ASP cc_start: 0.8496 (m-30) cc_final: 0.8182 (m-30) REVERT: C 155 ILE cc_start: 0.8254 (pt) cc_final: 0.7760 (mt) REVERT: C 212 MET cc_start: 0.9027 (ptm) cc_final: 0.8049 (pmm) REVERT: C 280 MET cc_start: 0.8975 (mpp) cc_final: 0.7550 (tpt) REVERT: C 449 MET cc_start: 0.7597 (tmm) cc_final: 0.7225 (tpp) REVERT: C 472 HIS cc_start: 0.8205 (m90) cc_final: 0.7905 (m-70) REVERT: C 536 MET cc_start: 0.8265 (pmm) cc_final: 0.7259 (tpt) REVERT: D 111 CYS cc_start: 0.8495 (t) cc_final: 0.8277 (t) REVERT: D 172 LEU cc_start: 0.9494 (mm) cc_final: 0.9176 (mm) REVERT: D 308 PHE cc_start: 0.8090 (m-10) cc_final: 0.7273 (m-10) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2304 time to fit residues: 66.6399 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 : 1.913 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 119 ASN ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.104215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077876 restraints weight = 61263.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080285 restraints weight = 41089.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082136 restraints weight = 30337.950| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12291 Z= 0.152 Angle : 0.680 10.749 16728 Z= 0.332 Chirality : 0.044 0.255 1874 Planarity : 0.005 0.053 2122 Dihedral : 6.185 59.832 1774 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.60 (0.22), residues: 1468 helix: 0.46 (0.50), residues: 107 sheet: 0.44 (0.21), residues: 588 loop : -1.22 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 109 HIS 0.007 0.001 HIS B 105 PHE 0.019 0.002 PHE A 198 TYR 0.016 0.002 TYR A 185 ARG 0.008 0.001 ARG B 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 5) link_NAG-ASN : angle 4.85690 ( 15) link_BETA1-4 : bond 0.00584 ( 3) link_BETA1-4 : angle 3.04856 ( 9) hydrogen bonds : bond 0.03816 ( 416) hydrogen bonds : angle 5.49606 ( 1146) SS BOND : bond 0.00270 ( 22) SS BOND : angle 1.67178 ( 44) covalent geometry : bond 0.00333 (12261) covalent geometry : angle 0.65667 (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 186 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.295 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: 0.9556 (tt) cc_final: 0.9234 (tt) REVERT: A 85 GLU cc_start: 0.9620 (mp0) cc_final: 0.9392 (pm20) REVERT: A 129 MET cc_start: 0.9640 (mpp) cc_final: 0.9385 (mpp) REVERT: B 102 LEU cc_start: 0.9218 (tp) cc_final: 0.8899 (tp) REVERT: B 136 ARG cc_start: 0.7823 (ttt-90) cc_final: 0.7567 (ttt-90) REVERT: B 204 LEU cc_start: 0.9110 (mp) cc_final: 0.8656 (pp) REVERT: B 218 TYR cc_start: 0.9077 (t80) cc_final: 0.8728 (t80) REVERT: B 241 MET cc_start: 0.3622 (tmm) cc_final: 0.2342 (ttt) REVERT: B 257 ASP cc_start: 0.9207 (p0) cc_final: 0.9003 (p0) REVERT: C 60 ASP cc_start: 0.8523 (m-30) cc_final: 0.8229 (m-30) REVERT: C 112 ASP cc_start: 0.7879 (p0) cc_final: 0.7582 (p0) REVERT: C 128 LEU cc_start: 0.9333 (pt) cc_final: 0.8943 (mm) REVERT: C 155 ILE cc_start: 0.8312 (pt) cc_final: 0.7822 (mt) REVERT: C 212 MET cc_start: 0.8864 (ptm) cc_final: 0.7927 (pmm) REVERT: C 449 MET cc_start: 0.7784 (tmm) cc_final: 0.7426 (tpp) REVERT: C 472 HIS cc_start: 0.8238 (m90) cc_final: 0.7952 (m-70) REVERT: C 536 MET cc_start: 0.8406 (pmm) cc_final: 0.7357 (tpt) REVERT: D 172 LEU cc_start: 0.9444 (mm) cc_final: 0.9134 (mm) REVERT: D 308 PHE cc_start: 0.8171 (m-10) cc_final: 0.7341 (m-10) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2166 time to fit residues: 60.0467 Evaluate side-chains 143 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 119 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.106676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080073 restraints weight = 60915.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082590 restraints weight = 40490.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084419 restraints weight = 29771.285| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 12291 Z= 0.110 Angle : 0.668 11.753 16728 Z= 0.322 Chirality : 0.044 0.338 1874 Planarity : 0.004 0.051 2122 Dihedral : 6.102 59.625 1774 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % 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: -0.52 (0.22), residues: 1468 helix: 0.54 (0.49), residues: 109 sheet: 0.51 (0.21), residues: 578 loop : -1.16 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 109 HIS 0.010 0.001 HIS B 105 PHE 0.013 0.001 PHE C 122 TYR 0.030 0.001 TYR B 187 ARG 0.010 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 5) link_NAG-ASN : angle 4.81634 ( 15) link_BETA1-4 : bond 0.00679 ( 3) link_BETA1-4 : angle 3.10587 ( 9) hydrogen bonds : bond 0.03540 ( 416) hydrogen bonds : angle 5.37972 ( 1146) SS BOND : bond 0.00229 ( 22) SS BOND : angle 1.50297 ( 44) covalent geometry : bond 0.00249 (12261) covalent geometry : angle 0.64475 (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 189 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.865 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: 0.9596 (tt) cc_final: 0.9310 (tt) REVERT: A 85 GLU cc_start: 0.9607 (mp0) cc_final: 0.9233 (pm20) REVERT: B 23 MET cc_start: 0.7207 (mmt) cc_final: 0.6163 (mmt) REVERT: B 119 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8578 (p0) REVERT: B 136 ARG cc_start: 0.7882 (ttt-90) cc_final: 0.7493 (ttt-90) REVERT: B 204 LEU cc_start: 0.8985 (mp) cc_final: 0.8525 (pp) REVERT: B 218 TYR cc_start: 0.8900 (t80) cc_final: 0.8028 (t80) REVERT: B 241 MET cc_start: 0.4061 (tmm) cc_final: 0.2984 (ttt) REVERT: C 60 ASP cc_start: 0.8515 (m-30) cc_final: 0.8175 (m-30) REVERT: C 112 ASP cc_start: 0.7614 (p0) cc_final: 0.7357 (p0) REVERT: C 128 LEU cc_start: 0.9340 (pt) cc_final: 0.8938 (mm) REVERT: C 155 ILE cc_start: 0.8202 (pt) cc_final: 0.7732 (mt) REVERT: C 212 MET cc_start: 0.9030 (ptm) cc_final: 0.8337 (pmm) REVERT: C 472 HIS cc_start: 0.8201 (m90) cc_final: 0.7924 (m-70) REVERT: C 536 MET cc_start: 0.8525 (pmm) cc_final: 0.7597 (tpt) REVERT: D 172 LEU cc_start: 0.9532 (mm) cc_final: 0.9218 (mm) REVERT: D 308 PHE cc_start: 0.8127 (m-10) cc_final: 0.7329 (m-10) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.3115 time to fit residues: 87.9285 Evaluate side-chains 148 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 108 optimal weight: 20.0000 chunk 139 optimal weight: 0.0370 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 119 ASN ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.107887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081387 restraints weight = 59514.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083981 restraints weight = 39753.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085888 restraints weight = 29168.863| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12291 Z= 0.103 Angle : 0.653 11.687 16728 Z= 0.314 Chirality : 0.044 0.343 1874 Planarity : 0.004 0.052 2122 Dihedral : 5.982 58.181 1774 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.41 (0.22), residues: 1468 helix: 0.62 (0.50), residues: 109 sheet: 0.63 (0.22), residues: 566 loop : -1.11 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 109 HIS 0.007 0.001 HIS B 105 PHE 0.013 0.001 PHE D 303 TYR 0.016 0.001 TYR B 187 ARG 0.009 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 5) link_NAG-ASN : angle 4.68277 ( 15) link_BETA1-4 : bond 0.00763 ( 3) link_BETA1-4 : angle 3.08114 ( 9) hydrogen bonds : bond 0.03445 ( 416) hydrogen bonds : angle 5.28403 ( 1146) SS BOND : bond 0.00260 ( 22) SS BOND : angle 1.39388 ( 44) covalent geometry : bond 0.00233 (12261) covalent geometry : angle 0.63120 (16660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.50 seconds wall clock time: 93 minutes 53.52 seconds (5633.52 seconds total)