Starting phenix.real_space_refine on Sat Oct 11 05:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oe0_16821/10_2025/8oe0_16821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oe0_16821/10_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_16821/10_2025/8oe0_16821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oe0_16821/10_2025/8oe0_16821.map" model { file = "/net/cci-nas-00/data/ceres_data/8oe0_16821/10_2025/8oe0_16821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oe0_16821/10_2025/8oe0_16821.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.28 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: 0.91 Conformation dependent library (CDL) restraints added in 661.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 2.22 Time building geometry restraints manager: 1.23 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: 0.910 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG A 38 TYR 0.029 0.001 TYR A 130 PHE 0.062 0.002 PHE A 134 TRP 0.033 0.002 TRP D 398 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00483 (12261) covalent geometry : angle 0.93411 (16660) SS BOND : bond 0.00396 ( 22) SS BOND : angle 1.97523 ( 44) hydrogen bonds : bond 0.11462 ( 416) hydrogen bonds : angle 7.12539 ( 1146) link_BETA1-4 : bond 0.00874 ( 3) link_BETA1-4 : angle 4.55292 ( 9) link_NAG-ASN : bond 0.00705 ( 5) link_NAG-ASN : angle 5.72135 ( 15) *********************** 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 : 0.488 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: 0.1178 time to fit residues: 41.5388 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 HIS ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 556 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 ASN ** 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 = 0.3917 r_free = 0.3917 target = 0.099894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.074373 restraints weight = 63803.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076482 restraints weight = 44068.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077956 restraints weight = 33447.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.079165 restraints weight = 27021.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.080058 restraints weight = 22774.111| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 12291 Z= 0.346 Angle : 0.943 12.225 16728 Z= 0.474 Chirality : 0.049 0.344 1874 Planarity : 0.006 0.052 2122 Dihedral : 7.741 59.849 1774 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 31.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.60 % Allowed : 8.13 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1468 helix: -1.12 (0.42), residues: 110 sheet: -0.19 (0.21), residues: 604 loop : -1.50 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 145 TYR 0.022 0.003 TYR B 88 PHE 0.033 0.004 PHE A 134 TRP 0.025 0.003 TRP D 244 HIS 0.013 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00713 (12261) covalent geometry : angle 0.92127 (16660) SS BOND : bond 0.00701 ( 22) SS BOND : angle 1.41319 ( 44) hydrogen bonds : bond 0.05864 ( 416) hydrogen bonds : angle 6.99878 ( 1146) link_BETA1-4 : bond 0.00746 ( 3) link_BETA1-4 : angle 3.45107 ( 9) link_NAG-ASN : bond 0.00727 ( 5) link_NAG-ASN : angle 5.95921 ( 15) *********************** 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 183 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.400 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: A 41 LEU cc_start: 0.9522 (tt) cc_final: 0.9231 (tt) REVERT: B 119 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8789 (p0) REVERT: B 172 LEU cc_start: 0.9670 (mp) cc_final: 0.9319 (pp) REVERT: B 190 SER cc_start: 0.8950 (p) cc_final: 0.8365 (t) REVERT: B 218 TYR cc_start: 0.9047 (t80) cc_final: 0.8658 (t80) REVERT: B 241 MET cc_start: 0.2705 (tmm) cc_final: 0.2416 (tmm) REVERT: B 294 PHE cc_start: 0.8700 (p90) cc_final: 0.8482 (p90) REVERT: C 60 ASP cc_start: 0.8584 (m-30) cc_final: 0.8261 (m-30) REVERT: C 155 ILE cc_start: 0.8357 (pt) cc_final: 0.7845 (mt) REVERT: C 212 MET cc_start: 0.8835 (ptm) cc_final: 0.7697 (pmm) REVERT: C 558 PHE cc_start: 0.8153 (m-10) cc_final: 0.7798 (m-10) REVERT: D 308 PHE cc_start: 0.8273 (m-10) cc_final: 0.7196 (m-10) REVERT: D 408 TRP cc_start: 0.8489 (m-90) cc_final: 0.8188 (m-90) REVERT: D 487 HIS cc_start: 0.8455 (m90) cc_final: 0.8199 (m90) outliers start: 8 outliers final: 4 residues processed: 181 average time/residue: 0.0937 time to fit residues: 25.4010 Evaluate side-chains 136 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 147 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 214 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.107059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081132 restraints weight = 63466.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083637 restraints weight = 41832.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085521 restraints weight = 30552.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086903 restraints weight = 23880.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.087872 restraints weight = 19658.204| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12291 Z= 0.132 Angle : 0.690 11.521 16728 Z= 0.338 Chirality : 0.046 0.323 1874 Planarity : 0.005 0.068 2122 Dihedral : 6.734 59.913 1774 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.21), residues: 1468 helix: 0.15 (0.47), residues: 106 sheet: 0.07 (0.21), residues: 586 loop : -1.33 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 38 TYR 0.053 0.002 TYR A 124 PHE 0.022 0.002 PHE A 134 TRP 0.013 0.001 TRP C 109 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (12261) covalent geometry : angle 0.66686 (16660) SS BOND : bond 0.00272 ( 22) SS BOND : angle 1.46266 ( 44) hydrogen bonds : bond 0.03956 ( 416) hydrogen bonds : angle 5.99253 ( 1146) link_BETA1-4 : bond 0.00300 ( 3) link_BETA1-4 : angle 3.56452 ( 9) link_NAG-ASN : bond 0.00534 ( 5) link_NAG-ASN : angle 4.79040 ( 15) *********************** 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 199 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.287 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: 0.9555 (tt) cc_final: 0.9296 (tt) REVERT: A 67 HIS cc_start: 0.8676 (t-90) cc_final: 0.8239 (t70) REVERT: A 124 TYR cc_start: 0.8242 (t80) cc_final: 0.7965 (t80) REVERT: A 129 MET cc_start: 0.9565 (mpp) cc_final: 0.9357 (mpp) REVERT: A 133 GLU cc_start: 0.8845 (pp20) cc_final: 0.8186 (pp20) REVERT: A 194 LEU cc_start: 0.8944 (mt) cc_final: 0.8422 (tp) REVERT: B 66 HIS cc_start: 0.8433 (t70) cc_final: 0.8204 (t70) REVERT: B 119 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8724 (p0) REVERT: B 136 ARG cc_start: 0.7992 (ttt-90) cc_final: 0.7301 (tmt-80) REVERT: B 137 PHE cc_start: 0.9003 (p90) cc_final: 0.8500 (p90) REVERT: B 190 SER cc_start: 0.8728 (p) cc_final: 0.7690 (t) REVERT: B 218 TYR cc_start: 0.9045 (t80) cc_final: 0.8239 (t80) REVERT: B 294 PHE cc_start: 0.8575 (p90) cc_final: 0.8372 (p90) REVERT: C 60 ASP cc_start: 0.8492 (m-30) cc_final: 0.8172 (m-30) REVERT: C 155 ILE cc_start: 0.8301 (pt) cc_final: 0.7842 (mt) REVERT: C 212 MET cc_start: 0.8855 (ptm) cc_final: 0.7700 (pmm) REVERT: C 449 MET cc_start: 0.7464 (tmm) cc_final: 0.6981 (tpp) REVERT: D 172 LEU cc_start: 0.9369 (mm) cc_final: 0.9045 (mm) REVERT: D 308 PHE cc_start: 0.8193 (m-10) cc_final: 0.7218 (m-10) REVERT: D 350 ILE cc_start: 0.9125 (mt) cc_final: 0.8828 (mt) REVERT: D 408 TRP cc_start: 0.8266 (m-90) cc_final: 0.7955 (m-90) outliers start: 2 outliers final: 0 residues processed: 199 average time/residue: 0.1041 time to fit residues: 29.9949 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 179 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** 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 = 0.4051 r_free = 0.4051 target = 0.107511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081043 restraints weight = 60320.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083642 restraints weight = 39523.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.085565 restraints weight = 28742.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086963 restraints weight = 22364.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088023 restraints weight = 18403.359| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12291 Z= 0.111 Angle : 0.643 11.297 16728 Z= 0.313 Chirality : 0.044 0.328 1874 Planarity : 0.004 0.052 2122 Dihedral : 6.309 59.748 1774 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.21), residues: 1468 helix: 0.61 (0.49), residues: 107 sheet: 0.15 (0.21), residues: 584 loop : -1.24 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 230 TYR 0.043 0.001 TYR A 124 PHE 0.015 0.001 PHE A 134 TRP 0.012 0.001 TRP C 244 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00244 (12261) covalent geometry : angle 0.62125 (16660) SS BOND : bond 0.00229 ( 22) SS BOND : angle 1.26410 ( 44) hydrogen bonds : bond 0.03631 ( 416) hydrogen bonds : angle 5.69459 ( 1146) link_BETA1-4 : bond 0.00496 ( 3) link_BETA1-4 : angle 3.23686 ( 9) link_NAG-ASN : bond 0.00487 ( 5) link_NAG-ASN : angle 4.70607 ( 15) *********************** 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 189 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.488 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: 0.9551 (tt) cc_final: 0.9297 (tt) REVERT: A 67 HIS cc_start: 0.8697 (t-90) cc_final: 0.8223 (t70) REVERT: B 66 HIS cc_start: 0.8493 (t70) cc_final: 0.8281 (t70) REVERT: B 102 LEU cc_start: 0.8650 (tp) cc_final: 0.8371 (tp) REVERT: B 136 ARG cc_start: 0.7858 (ttt-90) cc_final: 0.7524 (ttt-90) REVERT: B 190 SER cc_start: 0.8746 (p) cc_final: 0.8303 (p) REVERT: B 218 TYR cc_start: 0.8627 (t80) cc_final: 0.7907 (t80) REVERT: B 294 PHE cc_start: 0.8586 (p90) cc_final: 0.8326 (p90) REVERT: C 155 ILE cc_start: 0.8282 (pt) cc_final: 0.7794 (mt) REVERT: C 212 MET cc_start: 0.8886 (ptm) cc_final: 0.7719 (pmm) REVERT: C 223 MET cc_start: 0.8364 (pmm) cc_final: 0.7834 (pmm) REVERT: C 310 MET cc_start: 0.8026 (tmm) cc_final: 0.7701 (tmm) REVERT: C 449 MET cc_start: 0.7405 (tmm) cc_final: 0.7030 (tpp) REVERT: C 536 MET cc_start: 0.8189 (pmm) cc_final: 0.7788 (tpt) REVERT: D 172 LEU cc_start: 0.9529 (mm) cc_final: 0.9218 (mm) REVERT: D 178 ASN cc_start: 0.8200 (t0) cc_final: 0.7839 (t0) REVERT: D 308 PHE cc_start: 0.8153 (m-10) cc_final: 0.7213 (m-10) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1028 time to fit residues: 29.2025 Evaluate side-chains 159 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.106151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079140 restraints weight = 60093.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081701 restraints weight = 39713.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083549 restraints weight = 29069.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084955 restraints weight = 22913.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085973 restraints weight = 18932.529| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12291 Z= 0.129 Angle : 0.648 11.390 16728 Z= 0.318 Chirality : 0.044 0.333 1874 Planarity : 0.005 0.052 2122 Dihedral : 6.227 59.792 1774 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.21), residues: 1468 helix: 0.41 (0.48), residues: 109 sheet: 0.28 (0.21), residues: 596 loop : -1.27 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 314 TYR 0.014 0.001 TYR C 61 PHE 0.015 0.001 PHE C 122 TRP 0.011 0.001 TRP D 408 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00287 (12261) covalent geometry : angle 0.62599 (16660) SS BOND : bond 0.00280 ( 22) SS BOND : angle 1.28062 ( 44) hydrogen bonds : bond 0.03680 ( 416) hydrogen bonds : angle 5.61586 ( 1146) link_BETA1-4 : bond 0.00538 ( 3) link_BETA1-4 : angle 3.13304 ( 9) link_NAG-ASN : bond 0.00386 ( 5) link_NAG-ASN : angle 4.70456 ( 15) *********************** 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 188 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.488 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: 0.9546 (tt) cc_final: 0.9290 (tt) REVERT: A 67 HIS cc_start: 0.8760 (t-90) cc_final: 0.8376 (t-90) REVERT: A 124 TYR cc_start: 0.8564 (t80) cc_final: 0.8303 (t80) REVERT: B 37 TRP cc_start: 0.8543 (t-100) cc_final: 0.8343 (t-100) REVERT: B 108 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 136 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7364 (ttt-90) REVERT: B 190 SER cc_start: 0.8698 (p) cc_final: 0.7900 (t) REVERT: B 218 TYR cc_start: 0.8674 (t80) cc_final: 0.8007 (t80) REVERT: B 294 PHE cc_start: 0.8629 (p90) cc_final: 0.8371 (p90) REVERT: C 60 ASP cc_start: 0.8661 (m-30) cc_final: 0.8250 (m-30) REVERT: C 66 GLN cc_start: 0.9472 (pt0) cc_final: 0.9144 (pp30) REVERT: C 142 LEU cc_start: 0.8973 (mt) cc_final: 0.8720 (mt) REVERT: C 155 ILE cc_start: 0.8270 (pt) cc_final: 0.7784 (mt) REVERT: C 212 MET cc_start: 0.8977 (ptm) cc_final: 0.7915 (pmm) REVERT: C 223 MET cc_start: 0.8408 (pmm) cc_final: 0.7862 (pmm) REVERT: C 449 MET cc_start: 0.7476 (tmm) cc_final: 0.7106 (tpp) REVERT: C 536 MET cc_start: 0.8378 (pmm) cc_final: 0.7782 (tpt) REVERT: D 172 LEU cc_start: 0.9455 (mm) cc_final: 0.9121 (mm) REVERT: D 178 ASN cc_start: 0.8072 (t0) cc_final: 0.7740 (t0) REVERT: D 308 PHE cc_start: 0.8178 (m-10) cc_final: 0.7241 (m-10) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1068 time to fit residues: 29.6785 Evaluate side-chains 157 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.103619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077635 restraints weight = 61343.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079999 restraints weight = 40932.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081702 restraints weight = 30201.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082999 restraints weight = 23898.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083975 restraints weight = 19918.302| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3479 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= 0.164 Angle : 0.676 11.444 16728 Z= 0.333 Chirality : 0.044 0.346 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.292 58.947 1774 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.21), residues: 1468 helix: 0.27 (0.48), residues: 107 sheet: 0.20 (0.21), residues: 598 loop : -1.29 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 215 TYR 0.016 0.002 TYR A 185 PHE 0.020 0.002 PHE A 198 TRP 0.028 0.002 TRP C 109 HIS 0.012 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00357 (12261) covalent geometry : angle 0.65460 (16660) SS BOND : bond 0.00316 ( 22) SS BOND : angle 1.16580 ( 44) hydrogen bonds : bond 0.03866 ( 416) hydrogen bonds : angle 5.71603 ( 1146) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 3.05038 ( 9) link_NAG-ASN : bond 0.00372 ( 5) link_NAG-ASN : angle 4.88805 ( 15) *********************** 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 185 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.460 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 67 HIS cc_start: 0.8515 (t-90) cc_final: 0.8130 (t-90) REVERT: A 85 GLU cc_start: 0.9578 (mp0) cc_final: 0.9350 (pm20) REVERT: B 103 LEU cc_start: 0.8870 (mt) cc_final: 0.8609 (tp) REVERT: B 136 ARG cc_start: 0.7932 (ttt-90) cc_final: 0.7540 (ttt-90) REVERT: B 218 TYR cc_start: 0.8780 (t80) cc_final: 0.8172 (t80) REVERT: C 60 ASP cc_start: 0.8744 (m-30) cc_final: 0.8320 (m-30) REVERT: C 155 ILE cc_start: 0.8319 (pt) cc_final: 0.7827 (mt) REVERT: C 212 MET cc_start: 0.8895 (ptm) cc_final: 0.7974 (pmm) REVERT: C 223 MET cc_start: 0.8426 (pmm) cc_final: 0.7876 (pmm) REVERT: C 449 MET cc_start: 0.7611 (tmm) cc_final: 0.7061 (tpp) REVERT: C 472 HIS cc_start: 0.8373 (m90) cc_final: 0.8114 (m-70) REVERT: C 536 MET cc_start: 0.8314 (pmm) cc_final: 0.7806 (tpt) REVERT: D 172 LEU cc_start: 0.9474 (mm) cc_final: 0.9179 (mm) REVERT: D 178 ASN cc_start: 0.8135 (t0) cc_final: 0.7795 (t0) REVERT: D 308 PHE cc_start: 0.8228 (m-10) cc_final: 0.7272 (m-10) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1105 time to fit residues: 29.9180 Evaluate side-chains 146 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 36 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 352 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.104543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078409 restraints weight = 60593.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.080855 restraints weight = 40221.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082602 restraints weight = 29447.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083979 restraints weight = 23203.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.084890 restraints weight = 19184.755| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12291 Z= 0.121 Angle : 0.663 11.458 16728 Z= 0.322 Chirality : 0.045 0.375 1874 Planarity : 0.005 0.050 2122 Dihedral : 6.212 58.864 1774 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.22), residues: 1468 helix: 0.54 (0.49), residues: 107 sheet: 0.30 (0.21), residues: 580 loop : -1.23 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 213 TYR 0.011 0.001 TYR A 185 PHE 0.015 0.001 PHE A 198 TRP 0.028 0.001 TRP C 109 HIS 0.012 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00273 (12261) covalent geometry : angle 0.63955 (16660) SS BOND : bond 0.00282 ( 22) SS BOND : angle 1.38063 ( 44) hydrogen bonds : bond 0.03613 ( 416) hydrogen bonds : angle 5.55321 ( 1146) link_BETA1-4 : bond 0.00552 ( 3) link_BETA1-4 : angle 3.02818 ( 9) link_NAG-ASN : bond 0.00411 ( 5) link_NAG-ASN : angle 4.92925 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.530 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: 0.9495 (tt) cc_final: 0.9166 (tt) REVERT: A 67 HIS cc_start: 0.8289 (t-90) cc_final: 0.8055 (t-90) REVERT: A 85 GLU cc_start: 0.9578 (mp0) cc_final: 0.9186 (pm20) REVERT: B 36 ASP cc_start: 0.7896 (p0) cc_final: 0.7610 (p0) REVERT: B 136 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7519 (ttt-90) REVERT: C 155 ILE cc_start: 0.8332 (pt) cc_final: 0.7861 (mt) REVERT: C 212 MET cc_start: 0.8910 (ptm) cc_final: 0.8250 (pmm) REVERT: C 310 MET cc_start: 0.8052 (tmm) cc_final: 0.7831 (tmm) REVERT: C 449 MET cc_start: 0.7646 (tmm) cc_final: 0.7053 (tpp) REVERT: C 472 HIS cc_start: 0.8197 (m90) cc_final: 0.7922 (m-70) REVERT: C 536 MET cc_start: 0.8398 (pmm) cc_final: 0.7974 (tpt) REVERT: D 172 LEU cc_start: 0.9371 (mm) cc_final: 0.9058 (mm) REVERT: D 178 ASN cc_start: 0.8111 (t0) cc_final: 0.7774 (t0) REVERT: D 308 PHE cc_start: 0.8103 (m-10) cc_final: 0.7296 (m-10) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1051 time to fit residues: 29.1028 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 : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.0070 chunk 106 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.0050 chunk 138 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 41 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 overall best weight: 0.1408 ------------------------------------------------------------------------------- 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 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 173 GLN ** 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 = 0.4078 r_free = 0.4078 target = 0.108394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081848 restraints weight = 58780.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084528 restraints weight = 38389.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.086560 restraints weight = 27799.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088055 restraints weight = 21590.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.089146 restraints weight = 17640.754| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12291 Z= 0.108 Angle : 0.675 11.709 16728 Z= 0.325 Chirality : 0.045 0.342 1874 Planarity : 0.005 0.053 2122 Dihedral : 6.028 59.314 1774 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1468 helix: 0.71 (0.50), residues: 109 sheet: 0.51 (0.21), residues: 573 loop : -1.16 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 213 TYR 0.011 0.001 TYR A 124 PHE 0.013 0.001 PHE C 122 TRP 0.038 0.001 TRP C 109 HIS 0.010 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00236 (12261) covalent geometry : angle 0.65364 (16660) SS BOND : bond 0.00255 ( 22) SS BOND : angle 1.45468 ( 44) hydrogen bonds : bond 0.03408 ( 416) hydrogen bonds : angle 5.30132 ( 1146) link_BETA1-4 : bond 0.00707 ( 3) link_BETA1-4 : angle 3.03638 ( 9) link_NAG-ASN : bond 0.00611 ( 5) link_NAG-ASN : angle 4.59430 ( 15) *********************** 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 195 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.499 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: 0.9537 (tt) cc_final: 0.9228 (tt) REVERT: A 42 LYS cc_start: 0.9698 (ptmm) cc_final: 0.9478 (ptmm) REVERT: A 67 HIS cc_start: 0.8387 (t-90) cc_final: 0.7975 (t70) REVERT: A 85 GLU cc_start: 0.9525 (mp0) cc_final: 0.9132 (pm20) REVERT: A 129 MET cc_start: 0.9626 (mpp) cc_final: 0.9346 (mpp) REVERT: A 159 ILE cc_start: 0.9093 (tp) cc_final: 0.8686 (tp) REVERT: B 23 MET cc_start: 0.7105 (mmt) cc_final: 0.6086 (mmt) REVERT: B 36 ASP cc_start: 0.8181 (p0) cc_final: 0.7926 (p0) REVERT: B 37 TRP cc_start: 0.8541 (t-100) cc_final: 0.8086 (t-100) REVERT: B 136 ARG cc_start: 0.7834 (ttt-90) cc_final: 0.7473 (ttt-90) REVERT: B 241 MET cc_start: 0.4094 (tmm) cc_final: 0.2953 (ttt) REVERT: B 294 PHE cc_start: 0.8452 (p90) cc_final: 0.8198 (p90) REVERT: C 155 ILE cc_start: 0.8205 (pt) cc_final: 0.7764 (mt) REVERT: C 212 MET cc_start: 0.8890 (ptm) cc_final: 0.8264 (pmm) REVERT: C 447 ASN cc_start: 0.8702 (t0) cc_final: 0.8439 (t0) REVERT: C 449 MET cc_start: 0.7070 (tmm) cc_final: 0.6609 (tpp) REVERT: C 472 HIS cc_start: 0.8289 (m90) cc_final: 0.8081 (m-70) REVERT: C 536 MET cc_start: 0.8411 (pmm) cc_final: 0.7936 (tpt) REVERT: D 111 CYS cc_start: 0.8494 (t) cc_final: 0.8289 (t) REVERT: D 172 LEU cc_start: 0.9401 (mm) cc_final: 0.9091 (mm) REVERT: D 178 ASN cc_start: 0.8193 (t0) cc_final: 0.7826 (t0) REVERT: D 199 LEU cc_start: 0.8904 (mm) cc_final: 0.8676 (tp) REVERT: D 308 PHE cc_start: 0.7950 (m-10) cc_final: 0.7082 (m-10) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1024 time to fit residues: 29.7271 Evaluate side-chains 165 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 B 91 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080945 restraints weight = 61589.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.083460 restraints weight = 40859.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085402 restraints weight = 29766.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086805 restraints weight = 23334.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.087832 restraints weight = 19178.243| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12291 Z= 0.113 Angle : 0.663 11.923 16728 Z= 0.320 Chirality : 0.044 0.343 1874 Planarity : 0.004 0.049 2122 Dihedral : 5.960 57.797 1774 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.22), residues: 1468 helix: 0.85 (0.51), residues: 107 sheet: 0.61 (0.21), residues: 578 loop : -1.18 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 213 TYR 0.048 0.001 TYR A 124 PHE 0.012 0.001 PHE D 303 TRP 0.024 0.001 TRP C 109 HIS 0.014 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00260 (12261) covalent geometry : angle 0.64206 (16660) SS BOND : bond 0.00224 ( 22) SS BOND : angle 1.33744 ( 44) hydrogen bonds : bond 0.03483 ( 416) hydrogen bonds : angle 5.29699 ( 1146) link_BETA1-4 : bond 0.00612 ( 3) link_BETA1-4 : angle 2.89898 ( 9) link_NAG-ASN : bond 0.00448 ( 5) link_NAG-ASN : angle 4.68955 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.482 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: symmetry clash REVERT: A 41 LEU cc_start: 0.9535 (tt) cc_final: 0.9214 (tt) REVERT: A 42 LYS cc_start: 0.9699 (ptmm) cc_final: 0.9493 (ptmm) REVERT: A 67 HIS cc_start: 0.8437 (t-90) cc_final: 0.8125 (t-90) REVERT: A 85 GLU cc_start: 0.9591 (mp0) cc_final: 0.9193 (pm20) REVERT: B 23 MET cc_start: 0.6828 (mmt) cc_final: 0.5988 (mpp) REVERT: B 36 ASP cc_start: 0.8165 (p0) cc_final: 0.7914 (p0) REVERT: B 66 HIS cc_start: 0.8542 (t70) cc_final: 0.8341 (t70) REVERT: B 108 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7855 (mm-30) REVERT: B 136 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7504 (ttt-90) REVERT: B 204 LEU cc_start: 0.9317 (mm) cc_final: 0.8908 (pt) REVERT: B 241 MET cc_start: 0.4153 (tmm) cc_final: 0.2996 (ttt) REVERT: B 294 PHE cc_start: 0.8401 (p90) cc_final: 0.8142 (p90) REVERT: C 60 ASP cc_start: 0.8482 (m-30) cc_final: 0.8130 (m-30) REVERT: C 128 LEU cc_start: 0.9323 (pt) cc_final: 0.8591 (tp) REVERT: C 155 ILE cc_start: 0.8242 (pt) cc_final: 0.7784 (mt) REVERT: C 212 MET cc_start: 0.8903 (ptm) cc_final: 0.8292 (pmm) REVERT: C 472 HIS cc_start: 0.8311 (m90) cc_final: 0.8110 (m-70) REVERT: C 536 MET cc_start: 0.8368 (pmm) cc_final: 0.7948 (tpt) REVERT: D 172 LEU cc_start: 0.9390 (mm) cc_final: 0.9085 (mm) REVERT: D 178 ASN cc_start: 0.8194 (t0) cc_final: 0.7831 (t0) REVERT: D 199 LEU cc_start: 0.8931 (mm) cc_final: 0.8695 (tp) REVERT: D 308 PHE cc_start: 0.8063 (m-10) cc_final: 0.7212 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1020 time to fit residues: 29.5482 Evaluate side-chains 157 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 131 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.102682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076768 restraints weight = 64595.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079122 restraints weight = 43492.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.080850 restraints weight = 32327.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082151 restraints weight = 25582.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083117 restraints weight = 21201.353| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12291 Z= 0.168 Angle : 0.706 12.058 16728 Z= 0.346 Chirality : 0.045 0.312 1874 Planarity : 0.005 0.050 2122 Dihedral : 6.265 59.512 1774 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1468 helix: 0.36 (0.50), residues: 107 sheet: 0.35 (0.21), residues: 583 loop : -1.25 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 201 TYR 0.019 0.002 TYR A 185 PHE 0.024 0.002 PHE A 198 TRP 0.014 0.002 TRP B 37 HIS 0.012 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00369 (12261) covalent geometry : angle 0.68503 (16660) SS BOND : bond 0.00263 ( 22) SS BOND : angle 1.42178 ( 44) hydrogen bonds : bond 0.03888 ( 416) hydrogen bonds : angle 5.58995 ( 1146) link_BETA1-4 : bond 0.00532 ( 3) link_BETA1-4 : angle 2.88764 ( 9) link_NAG-ASN : bond 0.00317 ( 5) link_NAG-ASN : angle 4.79944 ( 15) ********************** 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 180 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.499 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: 0.9568 (tt) cc_final: 0.9313 (tt) REVERT: A 67 HIS cc_start: 0.8457 (t-90) cc_final: 0.8116 (t-90) REVERT: A 85 GLU cc_start: 0.9570 (mp0) cc_final: 0.9239 (pm20) REVERT: A 129 MET cc_start: 0.9598 (mpp) cc_final: 0.9340 (mpp) REVERT: B 23 MET cc_start: 0.7235 (mmt) cc_final: 0.6719 (mpp) REVERT: B 102 LEU cc_start: 0.9301 (tp) cc_final: 0.8896 (tp) REVERT: B 136 ARG cc_start: 0.7862 (ttt-90) cc_final: 0.6976 (ttt-90) REVERT: B 192 GLN cc_start: 0.7861 (tt0) cc_final: 0.7597 (tp40) REVERT: B 211 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6416 (mm-30) REVERT: B 241 MET cc_start: 0.3900 (tmm) cc_final: 0.2620 (ttt) REVERT: C 60 ASP cc_start: 0.8548 (m-30) cc_final: 0.8290 (m-30) REVERT: C 128 LEU cc_start: 0.9359 (pt) cc_final: 0.8924 (mm) REVERT: C 155 ILE cc_start: 0.8290 (pt) cc_final: 0.7810 (mt) REVERT: C 212 MET cc_start: 0.8941 (ptm) cc_final: 0.8452 (pmm) REVERT: C 472 HIS cc_start: 0.8444 (m90) cc_final: 0.8241 (m-70) REVERT: C 536 MET cc_start: 0.8383 (pmm) cc_final: 0.7888 (tpt) REVERT: D 172 LEU cc_start: 0.9487 (mm) cc_final: 0.9190 (mm) REVERT: D 178 ASN cc_start: 0.8251 (t0) cc_final: 0.7896 (t0) REVERT: D 308 PHE cc_start: 0.8134 (m-10) cc_final: 0.7284 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1023 time to fit residues: 27.6112 Evaluate side-chains 142 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 26 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 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 = 0.3982 r_free = 0.3982 target = 0.102443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076593 restraints weight = 63238.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078879 restraints weight = 42805.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080499 restraints weight = 31780.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081749 restraints weight = 25302.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082727 restraints weight = 21172.415| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12291 Z= 0.157 Angle : 0.697 11.806 16728 Z= 0.340 Chirality : 0.045 0.329 1874 Planarity : 0.005 0.061 2122 Dihedral : 6.342 58.355 1774 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.21), residues: 1468 helix: 0.27 (0.49), residues: 107 sheet: 0.24 (0.21), residues: 587 loop : -1.30 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 201 TYR 0.015 0.001 TYR A 185 PHE 0.022 0.002 PHE D 303 TRP 0.019 0.002 TRP C 109 HIS 0.011 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00341 (12261) covalent geometry : angle 0.67627 (16660) SS BOND : bond 0.00243 ( 22) SS BOND : angle 1.41419 ( 44) hydrogen bonds : bond 0.03833 ( 416) hydrogen bonds : angle 5.60952 ( 1146) link_BETA1-4 : bond 0.00538 ( 3) link_BETA1-4 : angle 2.93028 ( 9) link_NAG-ASN : bond 0.00339 ( 5) link_NAG-ASN : angle 4.82599 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.99 seconds wall clock time: 46 minutes 11.73 seconds (2771.73 seconds total)