Starting phenix.real_space_refine on Mon Dec 30 03:44:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oe0_16821/12_2024/8oe0_16821.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oe0_16821/12_2024/8oe0_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_16821/12_2024/8oe0_16821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oe0_16821/12_2024/8oe0_16821.map" model { file = "/net/cci-nas-00/data/ceres_data/8oe0_16821/12_2024/8oe0_16821.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oe0_16821/12_2024/8oe0_16821.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7524 2.51 5 N 2096 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2323 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3852 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4477 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 531} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.37, per 1000 atoms: 0.62 Number of scatterers: 11980 At special positions: 0 Unit cell: (95.13, 137.41, 197.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2279 8.00 N 2096 7.00 C 7524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 405 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.04 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 144 " " NAG D 801 " - " ASN D 224 " " NAG E 1 " - " ASN B 220 " " NAG F 1 " - " ASN C 463 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 34 sheets defined 8.9% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 4.247A pdb=" N GLN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.554A pdb=" N CYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 144 removed outlier: 3.583A pdb=" N CYS A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.776A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 463 through 468 removed outlier: 4.072A pdb=" N ALA C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 234 through 237 No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.875A pdb=" N GLU D 563 " --> pdb=" O PRO D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27 removed outlier: 5.509A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 33 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 35 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 107 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 92 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 27 removed outlier: 5.509A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 33 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 35 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 107 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.170A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.170A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 185 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154 Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 54 removed outlier: 6.235A pdb=" N ASP C 68 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN C 50 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN C 66 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 106 " --> pdb=" O CYS C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.860A pdb=" N ASN C 121 " --> pdb=" O CYS C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.860A pdb=" N ASN C 121 " --> pdb=" O CYS C 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB5, first strand: chain 'C' and resid 189 through 193 Processing sheet with id=AB6, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AB7, first strand: chain 'C' and resid 320 through 324 removed outlier: 3.951A pdb=" N LYS C 303 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA C 342 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR C 350 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB9, first strand: chain 'C' and resid 405 through 408 removed outlier: 3.866A pdb=" N LEU C 455 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 453 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 474 through 477 Processing sheet with id=AC2, first strand: chain 'C' and resid 514 through 519 removed outlier: 7.156A pdb=" N ASP C 544 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 514 through 519 removed outlier: 3.843A pdb=" N GLN C 540 " --> pdb=" O ARG C 505 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 507 " --> pdb=" O LYS C 538 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 538 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 42 removed outlier: 3.534A pdb=" N GLY D 134 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 72 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 80 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 74 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 196 through 198 removed outlier: 4.456A pdb=" N ASN D 159 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN D 142 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE D 239 " --> pdb=" O CYS D 145 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN D 147 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 188 Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 250 removed outlier: 3.831A pdb=" N ILE D 246 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN D 261 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 248 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 259 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 289 Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 348 removed outlier: 3.600A pdb=" N GLN D 348 " --> pdb=" O GLN D 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 387 through 393 removed outlier: 4.425A pdb=" N THR D 387 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP D 408 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 415 through 416 removed outlier: 3.631A pdb=" N GLY D 419 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.645A pdb=" N GLU D 447 " --> pdb=" O ASN D 451 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 488 through 491 Processing sheet with id=AD6, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AD7, first strand: chain 'D' and resid 585 through 590 442 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 3.27 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- 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 12261 Z= 0.315 Angle : 0.934 11.326 16660 Z= 0.544 Chirality : 0.058 0.502 1874 Planarity : 0.008 0.201 2122 Dihedral : 15.088 107.973 4646 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.37 % Allowed : 1.42 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1468 helix: 0.38 (0.52), residues: 105 sheet: 0.32 (0.21), residues: 600 loop : -1.42 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 398 HIS 0.005 0.001 HIS B 105 PHE 0.062 0.002 PHE A 134 TYR 0.029 0.001 TYR A 130 ARG 0.012 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 1.268 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: 0.2638 time to fit residues: 92.1786 Evaluate side-chains 168 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN A 206 ASN B 91 HIS C 355 HIS ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12261 Z= 0.198 Angle : 0.634 9.937 16660 Z= 0.319 Chirality : 0.044 0.382 1874 Planarity : 0.005 0.049 2122 Dihedral : 7.192 59.033 1774 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1468 helix: 0.52 (0.50), residues: 106 sheet: 0.40 (0.21), residues: 608 loop : -1.27 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 123 HIS 0.004 0.001 HIS A 146 PHE 0.037 0.002 PHE A 134 TYR 0.014 0.002 TYR C 143 ARG 0.004 0.001 ARG A 207 *********************** 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 205 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.410 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: 0.9603 (tt) cc_final: 0.9325 (tt) REVERT: A 42 LYS cc_start: 0.9714 (ptmm) cc_final: 0.9492 (ptmm) REVERT: A 159 ILE cc_start: 0.9096 (tp) cc_final: 0.8537 (tp) REVERT: B 24 TRP cc_start: 0.7780 (p90) cc_final: 0.7556 (p90) REVERT: B 136 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7321 (tmt-80) REVERT: B 172 LEU cc_start: 0.9632 (mp) cc_final: 0.9297 (pp) REVERT: B 190 SER cc_start: 0.8847 (p) cc_final: 0.7762 (t) REVERT: B 215 GLN cc_start: 0.9612 (tp-100) cc_final: 0.9267 (tt0) REVERT: B 218 TYR cc_start: 0.9098 (t80) cc_final: 0.8326 (t80) REVERT: B 294 PHE cc_start: 0.8809 (p90) cc_final: 0.8541 (p90) REVERT: C 50 ASN cc_start: 0.9107 (m-40) cc_final: 0.8859 (m110) REVERT: C 60 ASP cc_start: 0.8704 (m-30) cc_final: 0.8312 (m-30) REVERT: C 142 LEU cc_start: 0.8746 (mt) cc_final: 0.8501 (mt) REVERT: C 154 HIS cc_start: 0.7832 (m170) cc_final: 0.7428 (p90) REVERT: C 155 ILE cc_start: 0.8011 (pt) cc_final: 0.7422 (mt) REVERT: C 212 MET cc_start: 0.8663 (ptm) cc_final: 0.7897 (pmm) REVERT: C 223 MET cc_start: 0.8308 (pmm) cc_final: 0.7837 (pmm) REVERT: D 172 LEU cc_start: 0.9526 (mm) cc_final: 0.9162 (mm) REVERT: D 308 PHE cc_start: 0.8476 (m-10) cc_final: 0.7794 (m-10) REVERT: D 408 TRP cc_start: 0.8313 (m-90) cc_final: 0.7891 (m-90) outliers start: 2 outliers final: 1 residues processed: 205 average time/residue: 0.2400 time to fit residues: 72.2261 Evaluate side-chains 162 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 108 optimal weight: 7.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 138 ASN A 147 GLN B 91 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN D 309 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12261 Z= 0.262 Angle : 0.670 12.622 16660 Z= 0.335 Chirality : 0.044 0.327 1874 Planarity : 0.005 0.048 2122 Dihedral : 6.587 57.308 1774 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1468 helix: 0.07 (0.47), residues: 109 sheet: 0.35 (0.21), residues: 599 loop : -1.30 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 123 HIS 0.007 0.001 HIS A 67 PHE 0.023 0.002 PHE A 134 TYR 0.047 0.002 TYR A 124 ARG 0.015 0.001 ARG A 38 *********************** 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 193 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8596 (p0) cc_final: 0.8386 (p0) REVERT: A 129 MET cc_start: 0.9561 (mpp) cc_final: 0.9335 (mpp) REVERT: A 159 ILE cc_start: 0.9093 (tp) cc_final: 0.8735 (tp) REVERT: B 23 MET cc_start: 0.7463 (mmt) cc_final: 0.7247 (mpp) REVERT: B 172 LEU cc_start: 0.9589 (mp) cc_final: 0.9208 (pp) REVERT: B 190 SER cc_start: 0.8907 (p) cc_final: 0.8283 (t) REVERT: B 215 GLN cc_start: 0.9644 (tp-100) cc_final: 0.9437 (tp-100) REVERT: B 218 TYR cc_start: 0.8904 (t80) cc_final: 0.8140 (t80) REVERT: B 294 PHE cc_start: 0.8885 (p90) cc_final: 0.8621 (p90) REVERT: C 60 ASP cc_start: 0.8722 (m-30) cc_final: 0.8234 (m-30) REVERT: C 142 LEU cc_start: 0.8891 (mt) cc_final: 0.8662 (mt) REVERT: C 155 ILE cc_start: 0.8136 (pt) cc_final: 0.7481 (mt) REVERT: C 212 MET cc_start: 0.8708 (ptm) cc_final: 0.7581 (pmm) REVERT: C 223 MET cc_start: 0.8422 (pmm) cc_final: 0.7873 (pmm) REVERT: C 280 MET cc_start: 0.9294 (mpp) cc_final: 0.7902 (tpt) REVERT: C 449 MET cc_start: 0.7145 (tmm) cc_final: 0.6862 (tpp) REVERT: C 558 PHE cc_start: 0.8043 (m-10) cc_final: 0.7148 (m-10) REVERT: D 172 LEU cc_start: 0.9581 (mm) cc_final: 0.9243 (mm) REVERT: D 308 PHE cc_start: 0.8401 (m-10) cc_final: 0.7563 (m-10) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.2271 time to fit residues: 64.2407 Evaluate side-chains 153 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.0030 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12261 Z= 0.163 Angle : 0.620 9.792 16660 Z= 0.307 Chirality : 0.044 0.334 1874 Planarity : 0.004 0.047 2122 Dihedral : 6.190 57.905 1774 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1468 helix: 0.48 (0.48), residues: 107 sheet: 0.47 (0.21), residues: 597 loop : -1.27 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 123 HIS 0.005 0.001 HIS B 105 PHE 0.017 0.001 PHE A 134 TYR 0.024 0.001 TYR A 124 ARG 0.017 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9538 (tt) cc_final: 0.9223 (tt) REVERT: A 42 LYS cc_start: 0.9709 (ptmm) cc_final: 0.9501 (ptmm) REVERT: A 69 ASP cc_start: 0.9103 (p0) cc_final: 0.8684 (p0) REVERT: A 209 MET cc_start: 0.9509 (tmm) cc_final: 0.9130 (tpt) REVERT: B 66 HIS cc_start: 0.8702 (t70) cc_final: 0.8458 (t70) REVERT: B 137 PHE cc_start: 0.9076 (p90) cc_final: 0.8829 (p90) REVERT: B 190 SER cc_start: 0.8865 (p) cc_final: 0.8168 (t) REVERT: B 204 LEU cc_start: 0.9321 (mm) cc_final: 0.8787 (pp) REVERT: B 215 GLN cc_start: 0.9652 (tp-100) cc_final: 0.9240 (tt0) REVERT: B 218 TYR cc_start: 0.8826 (t80) cc_final: 0.8074 (t80) REVERT: B 294 PHE cc_start: 0.8842 (p90) cc_final: 0.8557 (p90) REVERT: C 60 ASP cc_start: 0.8719 (m-30) cc_final: 0.8264 (m-30) REVERT: C 72 ASP cc_start: 0.7741 (p0) cc_final: 0.7347 (p0) REVERT: C 128 LEU cc_start: 0.9129 (pt) cc_final: 0.8517 (tp) REVERT: C 142 LEU cc_start: 0.8859 (mt) cc_final: 0.8599 (mt) REVERT: C 155 ILE cc_start: 0.8031 (pt) cc_final: 0.7429 (mt) REVERT: C 212 MET cc_start: 0.8723 (ptm) cc_final: 0.7589 (pmm) REVERT: C 223 MET cc_start: 0.8433 (pmm) cc_final: 0.7868 (pmm) REVERT: C 280 MET cc_start: 0.9195 (mpp) cc_final: 0.7932 (tpt) REVERT: C 449 MET cc_start: 0.7127 (tmm) cc_final: 0.6857 (tpp) REVERT: C 558 PHE cc_start: 0.7735 (m-10) cc_final: 0.7334 (m-10) REVERT: D 172 LEU cc_start: 0.9492 (mm) cc_final: 0.9178 (mm) REVERT: D 178 ASN cc_start: 0.8140 (t0) cc_final: 0.7810 (t0) REVERT: D 308 PHE cc_start: 0.8299 (m-10) cc_final: 0.7408 (m-10) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2334 time to fit residues: 67.7972 Evaluate side-chains 156 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 87 HIS A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12261 Z= 0.307 Angle : 0.723 12.672 16660 Z= 0.363 Chirality : 0.046 0.334 1874 Planarity : 0.005 0.073 2122 Dihedral : 6.477 59.782 1774 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1468 helix: -0.45 (0.46), residues: 109 sheet: 0.08 (0.21), residues: 603 loop : -1.37 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 408 HIS 0.009 0.002 HIS A 67 PHE 0.024 0.002 PHE A 198 TYR 0.020 0.002 TYR A 185 ARG 0.009 0.001 ARG A 207 *********************** 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 182 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9607 (tt) cc_final: 0.9344 (tt) REVERT: A 42 LYS cc_start: 0.9707 (ptmm) cc_final: 0.9506 (ptmm) REVERT: A 209 MET cc_start: 0.9585 (tmm) cc_final: 0.9260 (tpt) REVERT: B 102 LEU cc_start: 0.8893 (tp) cc_final: 0.8615 (tp) REVERT: B 136 ARG cc_start: 0.7733 (ttt-90) cc_final: 0.7416 (ttt-90) REVERT: B 190 SER cc_start: 0.8944 (p) cc_final: 0.8213 (t) REVERT: B 218 TYR cc_start: 0.8899 (t80) cc_final: 0.8376 (t80) REVERT: B 241 MET cc_start: 0.3706 (tmm) cc_final: 0.2687 (ttt) REVERT: C 60 ASP cc_start: 0.8867 (m-30) cc_final: 0.8521 (m-30) REVERT: C 155 ILE cc_start: 0.8347 (pt) cc_final: 0.7751 (mt) REVERT: C 212 MET cc_start: 0.8764 (ptm) cc_final: 0.7611 (pmm) REVERT: C 223 MET cc_start: 0.8452 (pmm) cc_final: 0.7880 (pmm) REVERT: C 449 MET cc_start: 0.7454 (tmm) cc_final: 0.7079 (tpp) REVERT: C 472 HIS cc_start: 0.8440 (m90) cc_final: 0.8166 (m-70) REVERT: C 558 PHE cc_start: 0.7778 (m-10) cc_final: 0.7354 (m-10) REVERT: D 172 LEU cc_start: 0.9583 (mm) cc_final: 0.9279 (mm) REVERT: D 178 ASN cc_start: 0.8177 (t0) cc_final: 0.7969 (t0) REVERT: D 308 PHE cc_start: 0.8413 (m-10) cc_final: 0.7580 (m-10) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2367 time to fit residues: 63.4406 Evaluate side-chains 139 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 74 GLN A 138 ASN A 147 GLN A 206 ASN B 91 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 487 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12261 Z= 0.189 Angle : 0.647 9.341 16660 Z= 0.321 Chirality : 0.045 0.353 1874 Planarity : 0.005 0.049 2122 Dihedral : 6.250 59.946 1774 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1468 helix: -0.37 (0.46), residues: 115 sheet: 0.23 (0.21), residues: 589 loop : -1.27 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 112 HIS 0.014 0.001 HIS B 105 PHE 0.016 0.002 PHE A 198 TYR 0.013 0.002 TYR A 185 ARG 0.013 0.001 ARG A 38 *********************** 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 188 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.430 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: 0.9554 (tt) cc_final: 0.9325 (tt) REVERT: A 85 GLU cc_start: 0.9534 (mp0) cc_final: 0.9161 (pm20) REVERT: A 129 MET cc_start: 0.9635 (mpp) cc_final: 0.9427 (mpp) REVERT: A 209 MET cc_start: 0.9474 (tmm) cc_final: 0.9261 (tpt) REVERT: B 23 MET cc_start: 0.7024 (mmt) cc_final: 0.5824 (mmt) REVERT: B 136 ARG cc_start: 0.7860 (ttt-90) cc_final: 0.7399 (ttt-90) REVERT: B 137 PHE cc_start: 0.9049 (p90) cc_final: 0.8769 (p90) REVERT: B 190 SER cc_start: 0.8838 (p) cc_final: 0.8078 (t) REVERT: B 218 TYR cc_start: 0.8853 (t80) cc_final: 0.8305 (t80) REVERT: B 294 PHE cc_start: 0.8938 (p90) cc_final: 0.8669 (p90) REVERT: C 60 ASP cc_start: 0.8718 (m-30) cc_final: 0.8303 (m-30) REVERT: C 155 ILE cc_start: 0.8290 (pt) cc_final: 0.7725 (mt) REVERT: C 212 MET cc_start: 0.8639 (ptm) cc_final: 0.7616 (pmm) REVERT: C 280 MET cc_start: 0.9170 (mpp) cc_final: 0.7682 (tpt) REVERT: C 310 MET cc_start: 0.7982 (tmm) cc_final: 0.7661 (tmm) REVERT: C 449 MET cc_start: 0.7334 (tmm) cc_final: 0.6909 (tpp) REVERT: C 472 HIS cc_start: 0.8251 (m90) cc_final: 0.7972 (m-70) REVERT: D 172 LEU cc_start: 0.9565 (mm) cc_final: 0.9229 (mm) REVERT: D 178 ASN cc_start: 0.8193 (t0) cc_final: 0.7841 (t0) REVERT: D 308 PHE cc_start: 0.8311 (m-10) cc_final: 0.7474 (m-10) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2296 time to fit residues: 63.5183 Evaluate side-chains 151 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 109 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12261 Z= 0.259 Angle : 0.689 10.642 16660 Z= 0.343 Chirality : 0.045 0.407 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.361 56.691 1774 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1468 helix: -0.57 (0.46), residues: 113 sheet: 0.03 (0.21), residues: 598 loop : -1.29 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 37 HIS 0.012 0.001 HIS B 105 PHE 0.022 0.002 PHE A 198 TYR 0.018 0.002 TYR A 185 ARG 0.005 0.001 ARG A 38 *********************** 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 184 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.546 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: 0.9595 (tt) cc_final: 0.9296 (tt) REVERT: A 85 GLU cc_start: 0.9631 (mp0) cc_final: 0.9426 (pm20) REVERT: A 134 PHE cc_start: 0.9028 (m-80) cc_final: 0.8254 (m-80) REVERT: B 136 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7263 (ttt-90) REVERT: B 218 TYR cc_start: 0.8925 (t80) cc_final: 0.8336 (t80) REVERT: B 257 ASP cc_start: 0.9224 (p0) cc_final: 0.9016 (p0) REVERT: C 60 ASP cc_start: 0.8529 (m-30) cc_final: 0.8206 (m-30) REVERT: C 155 ILE cc_start: 0.8378 (pt) cc_final: 0.7855 (mt) REVERT: C 212 MET cc_start: 0.8826 (ptm) cc_final: 0.7853 (pmm) REVERT: C 280 MET cc_start: 0.9248 (mpp) cc_final: 0.7676 (tpt) REVERT: C 310 MET cc_start: 0.7990 (tmm) cc_final: 0.7636 (tmm) REVERT: C 449 MET cc_start: 0.7333 (tmm) cc_final: 0.6979 (tpp) REVERT: C 472 HIS cc_start: 0.7984 (m90) cc_final: 0.7690 (m-70) REVERT: C 558 PHE cc_start: 0.7778 (m-80) cc_final: 0.7489 (m-80) REVERT: D 172 LEU cc_start: 0.9569 (mm) cc_final: 0.9271 (mm) REVERT: D 178 ASN cc_start: 0.8261 (t0) cc_final: 0.7913 (t0) REVERT: D 308 PHE cc_start: 0.8351 (m-10) cc_final: 0.7525 (m-10) REVERT: D 487 HIS cc_start: 0.8844 (m-70) cc_final: 0.8616 (m90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2397 time to fit residues: 64.0165 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 : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 overall best weight: 2.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN ** A 206 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12261 Z= 0.234 Angle : 0.696 11.369 16660 Z= 0.343 Chirality : 0.046 0.337 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.391 56.656 1774 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1468 helix: -0.51 (0.45), residues: 115 sheet: 0.06 (0.21), residues: 589 loop : -1.29 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 112 HIS 0.013 0.001 HIS B 105 PHE 0.019 0.002 PHE A 198 TYR 0.015 0.002 TYR A 185 ARG 0.012 0.001 ARG C 466 *********************** 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 182 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.335 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: 0.9534 (tt) cc_final: 0.9291 (tt) REVERT: A 68 GLU cc_start: 0.8899 (pm20) cc_final: 0.8577 (pm20) REVERT: A 85 GLU cc_start: 0.9646 (mp0) cc_final: 0.9298 (pm20) REVERT: A 134 PHE cc_start: 0.9056 (m-80) cc_final: 0.8244 (m-80) REVERT: A 209 MET cc_start: 0.9548 (tmm) cc_final: 0.9340 (tpt) REVERT: B 23 MET cc_start: 0.7115 (mmt) cc_final: 0.5993 (mmt) REVERT: B 102 LEU cc_start: 0.9400 (tp) cc_final: 0.9144 (tp) REVERT: B 136 ARG cc_start: 0.7831 (ttt-90) cc_final: 0.7376 (ttt-90) REVERT: C 60 ASP cc_start: 0.8659 (m-30) cc_final: 0.8412 (m-30) REVERT: C 155 ILE cc_start: 0.8367 (pt) cc_final: 0.7864 (mt) REVERT: C 212 MET cc_start: 0.8835 (ptm) cc_final: 0.8314 (pmm) REVERT: C 280 MET cc_start: 0.9273 (mpp) cc_final: 0.7680 (tpp) REVERT: C 472 HIS cc_start: 0.8002 (m90) cc_final: 0.7783 (m90) REVERT: C 558 PHE cc_start: 0.7693 (m-80) cc_final: 0.7423 (m-80) REVERT: D 172 LEU cc_start: 0.9559 (mm) cc_final: 0.9234 (mm) REVERT: D 178 ASN cc_start: 0.8402 (t0) cc_final: 0.8087 (t0) REVERT: D 308 PHE cc_start: 0.8289 (m-10) cc_final: 0.7428 (m-10) REVERT: D 487 HIS cc_start: 0.8840 (m-70) cc_final: 0.8621 (m-70) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2339 time to fit residues: 62.2161 Evaluate side-chains 145 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.0770 chunk 137 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12261 Z= 0.180 Angle : 0.665 10.153 16660 Z= 0.327 Chirality : 0.045 0.336 1874 Planarity : 0.005 0.061 2122 Dihedral : 6.293 57.072 1774 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1468 helix: 0.06 (0.48), residues: 107 sheet: 0.17 (0.21), residues: 583 loop : -1.23 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 398 HIS 0.005 0.001 HIS B 105 PHE 0.014 0.001 PHE A 198 TYR 0.012 0.001 TYR B 218 ARG 0.011 0.001 ARG A 38 *********************** 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 177 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.409 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: 0.9578 (tt) cc_final: 0.9267 (tt) REVERT: A 42 LYS cc_start: 0.9701 (ptmm) cc_final: 0.9499 (ptmm) REVERT: A 85 GLU cc_start: 0.9614 (mp0) cc_final: 0.9292 (pm20) REVERT: A 129 MET cc_start: 0.9628 (mpp) cc_final: 0.9338 (mpp) REVERT: B 82 PHE cc_start: 0.8195 (m-80) cc_final: 0.7759 (m-80) REVERT: B 102 LEU cc_start: 0.9334 (tp) cc_final: 0.9040 (tp) REVERT: B 136 ARG cc_start: 0.7902 (ttt-90) cc_final: 0.7513 (ttt-90) REVERT: B 204 LEU cc_start: 0.9213 (mp) cc_final: 0.8859 (pt) REVERT: B 257 ASP cc_start: 0.9182 (p0) cc_final: 0.8970 (p0) REVERT: C 60 ASP cc_start: 0.8599 (m-30) cc_final: 0.8366 (m-30) REVERT: C 155 ILE cc_start: 0.8323 (pt) cc_final: 0.7818 (mt) REVERT: C 212 MET cc_start: 0.8857 (ptm) cc_final: 0.8352 (pmm) REVERT: C 280 MET cc_start: 0.8906 (mpp) cc_final: 0.7639 (tpp) REVERT: C 472 HIS cc_start: 0.7847 (m90) cc_final: 0.7633 (m90) REVERT: D 172 LEU cc_start: 0.9602 (mm) cc_final: 0.9271 (mm) REVERT: D 178 ASN cc_start: 0.8236 (t0) cc_final: 0.7900 (t0) REVERT: D 308 PHE cc_start: 0.8183 (m-10) cc_final: 0.7468 (m-10) REVERT: D 487 HIS cc_start: 0.8922 (m-70) cc_final: 0.8705 (m-70) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2206 time to fit residues: 58.7684 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 : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 119 ASN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12261 Z= 0.252 Angle : 0.703 11.451 16660 Z= 0.347 Chirality : 0.045 0.321 1874 Planarity : 0.005 0.052 2122 Dihedral : 6.418 56.758 1774 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1468 helix: -0.26 (0.47), residues: 107 sheet: 0.06 (0.21), residues: 591 loop : -1.34 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 398 HIS 0.006 0.001 HIS D 487 PHE 0.020 0.002 PHE A 198 TYR 0.021 0.002 TYR C 502 ARG 0.007 0.001 ARG A 38 ********************** 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 176 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.384 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: 0.9540 (tt) cc_final: 0.9291 (tt) REVERT: A 85 GLU cc_start: 0.9633 (mp0) cc_final: 0.9323 (pm20) REVERT: A 134 PHE cc_start: 0.9062 (m-10) cc_final: 0.8271 (m-80) REVERT: B 82 PHE cc_start: 0.8314 (m-80) cc_final: 0.7902 (m-80) REVERT: B 119 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8691 (p0) REVERT: B 136 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7301 (ttt-90) REVERT: B 204 LEU cc_start: 0.9232 (mp) cc_final: 0.8863 (pt) REVERT: B 216 ASN cc_start: 0.9331 (m-40) cc_final: 0.9105 (m-40) REVERT: B 241 MET cc_start: 0.4016 (tmm) cc_final: 0.2939 (ttt) REVERT: C 60 ASP cc_start: 0.8759 (m-30) cc_final: 0.8377 (m-30) REVERT: C 155 ILE cc_start: 0.8311 (pt) cc_final: 0.7778 (mt) REVERT: C 212 MET cc_start: 0.8910 (ptm) cc_final: 0.8437 (pmm) REVERT: C 466 ARG cc_start: 0.9498 (ptp90) cc_final: 0.9263 (ptt-90) REVERT: C 472 HIS cc_start: 0.8046 (m90) cc_final: 0.7832 (m90) REVERT: C 558 PHE cc_start: 0.7693 (m-80) cc_final: 0.7443 (m-80) REVERT: D 172 LEU cc_start: 0.9561 (mm) cc_final: 0.9271 (mm) REVERT: D 178 ASN cc_start: 0.8541 (t0) cc_final: 0.8199 (t0) REVERT: D 298 ARG cc_start: 0.7003 (mmp80) cc_final: 0.6432 (mpt180) REVERT: D 308 PHE cc_start: 0.8113 (m-10) cc_final: 0.7373 (m-10) REVERT: D 487 HIS cc_start: 0.8928 (m-70) cc_final: 0.8699 (m-70) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2193 time to fit residues: 58.2342 Evaluate side-chains 140 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 138 ASN A 147 GLN A 206 ASN B 119 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.103712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078051 restraints weight = 61984.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.080482 restraints weight = 41521.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082246 restraints weight = 30672.973| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12261 Z= 0.179 Angle : 0.653 9.171 16660 Z= 0.322 Chirality : 0.045 0.324 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.301 58.647 1774 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.07 % Allowed : 0.60 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1468 helix: -0.04 (0.47), residues: 109 sheet: 0.25 (0.22), residues: 577 loop : -1.24 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 398 HIS 0.007 0.001 HIS B 105 PHE 0.014 0.001 PHE D 303 TYR 0.009 0.001 TYR A 185 ARG 0.008 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.76 seconds wall clock time: 47 minutes 19.96 seconds (2839.96 seconds total)