Starting phenix.real_space_refine on Thu Feb 15 10:34:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_2024/8oe0_16821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_2024/8oe0_16821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_2024/8oe0_16821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_2024/8oe0_16821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oe0_16821/02_2024/8oe0_16821.pdb" } 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 Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2323 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3852 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4477 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 531} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.84, per 1000 atoms: 0.57 Number of scatterers: 11980 At special positions: 0 Unit cell: (95.13, 137.41, 197.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2279 8.00 N 2096 7.00 C 7524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.04 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.02 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 405 " distance=2.04 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.04 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.04 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.76 Conformation dependent library (CDL) restraints added in 2.4 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: 1.60 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: 4.25 Time building geometry restraints manager: 5.16 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: 96.45 - 104.07: 218 104.07 - 111.69: 5665 111.69 - 119.31: 4636 119.31 - 126.93: 5923 126.93 - 134.55: 218 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 2.440 nonbonded pdb=" O ASP D 450 " pdb=" OG SER D 501 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 231 " pdb=" OG SER B 321 " model vdw 2.249 2.440 nonbonded pdb=" NZ LYS C 147 " pdb=" O TRP C 244 " model vdw 2.269 2.520 nonbonded pdb=" N MET B 23 " pdb=" O VAL B 32 " model vdw 2.269 2.520 ... (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 ========== 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 35.870 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.580 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 1.509 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: 0.2739 time to fit residues: 94.8815 Evaluate side-chains 168 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 0.0970 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12261 Z= 0.164 Angle : 0.601 10.160 16660 Z= 0.300 Chirality : 0.043 0.390 1874 Planarity : 0.004 0.049 2122 Dihedral : 7.297 60.483 1774 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.07 % Allowed : 5.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1468 helix: 0.67 (0.51), residues: 106 sheet: 0.39 (0.21), residues: 613 loop : -1.26 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 123 HIS 0.005 0.001 HIS B 91 PHE 0.035 0.002 PHE A 134 TYR 0.012 0.001 TYR C 502 ARG 0.004 0.000 ARG A 201 *********************** 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 fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.358 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 39 ASN cc_start: 0.9563 (m-40) cc_final: 0.9357 (m-40) REVERT: A 41 LEU cc_start: 0.9607 (tt) cc_final: 0.9337 (tt) REVERT: A 42 LYS cc_start: 0.9733 (ptmm) cc_final: 0.9231 (tppt) REVERT: A 159 ILE cc_start: 0.9055 (tp) cc_final: 0.8497 (tp) REVERT: B 136 ARG cc_start: 0.7895 (ttt-90) cc_final: 0.7403 (tmm-80) REVERT: B 137 PHE cc_start: 0.9039 (p90) cc_final: 0.8616 (p90) REVERT: B 172 LEU cc_start: 0.9610 (mp) cc_final: 0.9279 (pp) REVERT: B 190 SER cc_start: 0.8755 (p) cc_final: 0.8280 (t) REVERT: B 215 GLN cc_start: 0.9602 (tp-100) cc_final: 0.9278 (tt0) REVERT: B 218 TYR cc_start: 0.9058 (t80) cc_final: 0.8305 (t80) REVERT: B 294 PHE cc_start: 0.8763 (p90) cc_final: 0.8367 (p90) REVERT: C 50 ASN cc_start: 0.9088 (m-40) cc_final: 0.8837 (m110) REVERT: C 60 ASP cc_start: 0.8703 (m-30) cc_final: 0.8242 (m-30) REVERT: C 117 LEU cc_start: 0.8907 (mm) cc_final: 0.8703 (mm) REVERT: C 142 LEU cc_start: 0.8533 (mt) cc_final: 0.8211 (mt) REVERT: C 154 HIS cc_start: 0.7760 (m170) cc_final: 0.7369 (p90) REVERT: C 155 ILE cc_start: 0.7963 (pt) cc_final: 0.7377 (mt) REVERT: C 212 MET cc_start: 0.8646 (ptm) cc_final: 0.7911 (pmm) REVERT: C 223 MET cc_start: 0.8330 (pmm) cc_final: 0.7823 (pmm) REVERT: D 172 LEU cc_start: 0.9511 (mm) cc_final: 0.9138 (mm) REVERT: D 308 PHE cc_start: 0.8461 (m-10) cc_final: 0.7769 (m-10) REVERT: D 408 TRP cc_start: 0.8296 (m-90) cc_final: 0.7950 (m-90) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2655 time to fit residues: 79.0022 Evaluate side-chains 159 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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: 10.0000 chunk 41 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 67 HIS A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** C 107 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** D 309 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12261 Z= 0.236 Angle : 0.643 12.348 16660 Z= 0.321 Chirality : 0.043 0.365 1874 Planarity : 0.005 0.073 2122 Dihedral : 6.671 55.737 1774 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.25 % 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: -0.65 (0.21), residues: 1468 helix: 0.29 (0.47), residues: 107 sheet: 0.39 (0.21), residues: 615 loop : -1.27 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 123 HIS 0.006 0.001 HIS A 67 PHE 0.022 0.002 PHE A 134 TYR 0.047 0.002 TYR A 124 ARG 0.005 0.001 ARG A 207 *********************** 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 fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9582 (tt) cc_final: 0.9359 (tt) REVERT: A 129 MET cc_start: 0.9531 (mpp) cc_final: 0.9322 (mpp) REVERT: A 159 ILE cc_start: 0.9046 (tp) cc_final: 0.8671 (tp) REVERT: B 136 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7542 (tmt-80) REVERT: B 190 SER cc_start: 0.8819 (p) cc_final: 0.7887 (t) REVERT: B 215 GLN cc_start: 0.9637 (tp-100) cc_final: 0.9418 (tp-100) REVERT: B 218 TYR cc_start: 0.8906 (t80) cc_final: 0.8309 (t80) REVERT: B 294 PHE cc_start: 0.8910 (p90) cc_final: 0.8630 (p90) REVERT: C 50 ASN cc_start: 0.9021 (m-40) cc_final: 0.8741 (m110) REVERT: C 60 ASP cc_start: 0.8678 (m-30) cc_final: 0.8148 (m-30) REVERT: C 142 LEU cc_start: 0.8772 (mt) cc_final: 0.8551 (mt) REVERT: C 152 LEU cc_start: 0.8651 (tp) cc_final: 0.8445 (tp) REVERT: C 155 ILE cc_start: 0.7960 (pt) cc_final: 0.7292 (mt) REVERT: C 212 MET cc_start: 0.8585 (ptm) cc_final: 0.7816 (pmm) REVERT: C 223 MET cc_start: 0.8451 (pmm) cc_final: 0.7846 (pmm) REVERT: C 558 PHE cc_start: 0.8039 (m-10) cc_final: 0.7126 (m-10) REVERT: D 172 LEU cc_start: 0.9604 (mm) cc_final: 0.9278 (mm) REVERT: D 308 PHE cc_start: 0.8405 (m-10) cc_final: 0.7715 (m-10) REVERT: D 408 TRP cc_start: 0.8335 (m-90) cc_final: 0.7881 (m-90) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2309 time to fit residues: 65.4130 Evaluate side-chains 151 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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: 6.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 144 optimal weight: 0.0470 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12261 Z= 0.325 Angle : 0.745 14.321 16660 Z= 0.375 Chirality : 0.045 0.388 1874 Planarity : 0.005 0.047 2122 Dihedral : 6.902 58.239 1774 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.30 % Allowed : 6.57 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), residues: 1468 helix: -1.22 (0.41), residues: 116 sheet: -0.00 (0.21), residues: 604 loop : -1.35 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 380 HIS 0.008 0.002 HIS A 67 PHE 0.030 0.003 PHE A 198 TYR 0.038 0.002 TYR A 124 ARG 0.026 0.001 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 188 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.460 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: A 42 LYS cc_start: 0.9700 (ptmm) cc_final: 0.9496 (ptmm) REVERT: A 134 PHE cc_start: 0.9159 (m-80) cc_final: 0.8234 (m-80) REVERT: A 189 MET cc_start: 0.8393 (mmp) cc_final: 0.8097 (mmm) REVERT: A 209 MET cc_start: 0.9584 (tmm) cc_final: 0.9181 (tpt) REVERT: B 102 LEU cc_start: 0.8824 (tp) cc_final: 0.8526 (tp) REVERT: B 136 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7452 (ttt-90) REVERT: B 190 SER cc_start: 0.8850 (p) cc_final: 0.8160 (t) REVERT: C 60 ASP cc_start: 0.8884 (m-30) cc_final: 0.8493 (m-30) REVERT: C 155 ILE cc_start: 0.8347 (pt) cc_final: 0.7782 (mt) REVERT: C 212 MET cc_start: 0.8617 (ptm) cc_final: 0.7569 (pmm) REVERT: C 310 MET cc_start: 0.7829 (tmm) cc_final: 0.7608 (tmm) REVERT: C 472 HIS cc_start: 0.8430 (m90) cc_final: 0.8160 (m-70) REVERT: C 558 PHE cc_start: 0.7755 (m-10) cc_final: 0.7303 (m-10) REVERT: D 172 LEU cc_start: 0.9602 (mm) cc_final: 0.9387 (mm) REVERT: D 178 ASN cc_start: 0.8252 (t0) cc_final: 0.7928 (p0) REVERT: D 308 PHE cc_start: 0.8416 (m-10) cc_final: 0.7552 (m-10) REVERT: D 487 HIS cc_start: 0.8689 (m90) cc_final: 0.8462 (m90) outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 0.2393 time to fit residues: 64.9435 Evaluate side-chains 148 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 6.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 67 HIS A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 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: 0.7080 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12261 Z= 0.350 Angle : 0.780 13.579 16660 Z= 0.394 Chirality : 0.048 0.372 1874 Planarity : 0.006 0.059 2122 Dihedral : 7.082 57.264 1774 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.10 % 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: -1.46 (0.21), residues: 1468 helix: -1.44 (0.41), residues: 116 sheet: -0.22 (0.21), residues: 604 loop : -1.50 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 408 HIS 0.009 0.002 HIS A 67 PHE 0.029 0.003 PHE A 198 TYR 0.038 0.002 TYR A 124 ARG 0.016 0.001 ARG A 38 *********************** 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 175 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.367 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 134 PHE cc_start: 0.9131 (m-80) cc_final: 0.8209 (m-80) REVERT: A 189 MET cc_start: 0.8524 (mmp) cc_final: 0.8269 (mmm) REVERT: B 125 PHE cc_start: 0.9046 (m-80) cc_final: 0.8820 (m-10) REVERT: B 136 ARG cc_start: 0.7764 (ttt-90) cc_final: 0.7449 (ttt-90) REVERT: B 190 SER cc_start: 0.8965 (p) cc_final: 0.8298 (t) REVERT: B 208 LEU cc_start: 0.8411 (mm) cc_final: 0.8203 (mm) REVERT: B 241 MET cc_start: 0.4038 (tmm) cc_final: 0.2879 (ttt) REVERT: C 60 ASP cc_start: 0.8715 (m-30) cc_final: 0.8408 (m-30) REVERT: C 136 GLN cc_start: 0.7867 (tp40) cc_final: 0.7435 (tp40) REVERT: C 155 ILE cc_start: 0.8521 (pt) cc_final: 0.8033 (mt) REVERT: C 212 MET cc_start: 0.8510 (ptm) cc_final: 0.7512 (pmm) REVERT: C 280 MET cc_start: 0.8509 (mmp) cc_final: 0.6539 (tpp) REVERT: C 310 MET cc_start: 0.7877 (tmm) cc_final: 0.7536 (tmm) REVERT: C 472 HIS cc_start: 0.7987 (m90) cc_final: 0.7686 (m-70) REVERT: D 172 LEU cc_start: 0.9631 (mm) cc_final: 0.9385 (mm) REVERT: D 178 ASN cc_start: 0.8569 (t0) cc_final: 0.8335 (p0) REVERT: D 199 LEU cc_start: 0.8746 (mm) cc_final: 0.8485 (tp) REVERT: D 308 PHE cc_start: 0.8149 (m-10) cc_final: 0.7385 (m-10) REVERT: D 487 HIS cc_start: 0.8640 (m90) cc_final: 0.8405 (m90) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2387 time to fit residues: 60.4451 Evaluate side-chains 134 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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: 10.0000 chunk 129 optimal weight: 8.9990 chunk 28 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 67 HIS A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12261 Z= 0.177 Angle : 0.663 9.227 16660 Z= 0.328 Chirality : 0.045 0.358 1874 Planarity : 0.005 0.049 2122 Dihedral : 6.662 56.847 1774 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % 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: -1.12 (0.21), residues: 1468 helix: -0.69 (0.44), residues: 116 sheet: -0.03 (0.21), residues: 601 loop : -1.34 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.006 0.001 HIS B 105 PHE 0.015 0.002 PHE A 198 TYR 0.029 0.002 TYR A 124 ARG 0.011 0.000 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 186 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.561 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 39 ASN cc_start: 0.9657 (m110) cc_final: 0.9428 (m-40) REVERT: A 41 LEU cc_start: 0.9535 (tt) cc_final: 0.9300 (tt) REVERT: A 134 PHE cc_start: 0.8975 (m-80) cc_final: 0.8256 (m-80) REVERT: A 209 MET cc_start: 0.9432 (tmm) cc_final: 0.8984 (tpt) REVERT: B 136 ARG cc_start: 0.7760 (ttt-90) cc_final: 0.7267 (ttt-90) REVERT: B 137 PHE cc_start: 0.9089 (p90) cc_final: 0.8819 (p90) REVERT: B 190 SER cc_start: 0.8785 (p) cc_final: 0.8090 (t) REVERT: B 215 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9256 (tt0) REVERT: B 218 TYR cc_start: 0.8929 (t80) cc_final: 0.8692 (t80) REVERT: C 60 ASP cc_start: 0.8698 (m-30) cc_final: 0.8193 (m-30) REVERT: C 155 ILE cc_start: 0.8520 (pt) cc_final: 0.8030 (mt) REVERT: C 212 MET cc_start: 0.8550 (ptm) cc_final: 0.7657 (pmm) REVERT: C 280 MET cc_start: 0.8179 (mmp) cc_final: 0.6180 (tpp) REVERT: C 310 MET cc_start: 0.7758 (tmm) cc_final: 0.7526 (tmm) REVERT: C 472 HIS cc_start: 0.7977 (m90) cc_final: 0.7756 (m90) REVERT: D 172 LEU cc_start: 0.9580 (mm) cc_final: 0.9306 (mm) REVERT: D 178 ASN cc_start: 0.8529 (t0) cc_final: 0.8162 (t0) REVERT: D 308 PHE cc_start: 0.8243 (m-10) cc_final: 0.7414 (m-10) REVERT: D 487 HIS cc_start: 0.8780 (m90) cc_final: 0.8572 (m90) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2347 time to fit residues: 63.8515 Evaluate side-chains 149 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 138 ASN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 109 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 12261 Z= 0.340 Angle : 0.768 11.956 16660 Z= 0.383 Chirality : 0.046 0.356 1874 Planarity : 0.005 0.051 2122 Dihedral : 6.908 56.956 1774 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 32.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % 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: -1.45 (0.21), residues: 1468 helix: -1.08 (0.42), residues: 116 sheet: -0.34 (0.21), residues: 614 loop : -1.45 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 37 HIS 0.008 0.002 HIS B 105 PHE 0.025 0.002 PHE A 198 TYR 0.024 0.002 TYR A 185 ARG 0.007 0.001 ARG D 394 *********************** 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 176 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.407 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 110 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5651 (pp30) REVERT: A 116 MET cc_start: 0.9447 (mmp) cc_final: 0.9229 (mmm) REVERT: A 134 PHE cc_start: 0.9064 (m-80) cc_final: 0.8271 (m-80) REVERT: B 108 GLU cc_start: 0.9354 (tm-30) cc_final: 0.8580 (mm-30) REVERT: B 136 ARG cc_start: 0.7767 (ttt-90) cc_final: 0.7474 (ttt-90) REVERT: B 190 SER cc_start: 0.8943 (p) cc_final: 0.8311 (t) REVERT: B 241 MET cc_start: 0.3855 (tmm) cc_final: 0.2975 (ttt) REVERT: C 60 ASP cc_start: 0.8853 (m-30) cc_final: 0.8635 (m-30) REVERT: C 136 GLN cc_start: 0.8019 (tp40) cc_final: 0.7629 (tp-100) REVERT: C 155 ILE cc_start: 0.8562 (pt) cc_final: 0.8098 (mt) REVERT: C 212 MET cc_start: 0.8308 (ptm) cc_final: 0.7462 (pmm) REVERT: C 280 MET cc_start: 0.8461 (mmp) cc_final: 0.6641 (tpp) REVERT: C 310 MET cc_start: 0.7820 (tmm) cc_final: 0.7432 (tmm) REVERT: C 449 MET cc_start: 0.7103 (tmm) cc_final: 0.6721 (tpp) REVERT: D 178 ASN cc_start: 0.8609 (t0) cc_final: 0.8247 (t0) REVERT: D 308 PHE cc_start: 0.8077 (m-10) cc_final: 0.7130 (m-10) REVERT: D 487 HIS cc_start: 0.8757 (m90) cc_final: 0.8548 (m90) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2412 time to fit residues: 62.2716 Evaluate side-chains 135 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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: 3.9990 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 339 ASN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12261 Z= 0.213 Angle : 0.690 9.881 16660 Z= 0.341 Chirality : 0.046 0.367 1874 Planarity : 0.005 0.058 2122 Dihedral : 6.659 56.997 1774 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.07 % Allowed : 1.79 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1468 helix: -0.63 (0.45), residues: 110 sheet: -0.16 (0.21), residues: 593 loop : -1.40 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 112 HIS 0.015 0.001 HIS B 105 PHE 0.018 0.002 PHE A 198 TYR 0.014 0.002 TYR A 185 ARG 0.017 0.001 ARG A 38 *********************** 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 176 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.520 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 39 ASN cc_start: 0.9673 (m110) cc_final: 0.9444 (m-40) REVERT: A 41 LEU cc_start: 0.9510 (tt) cc_final: 0.9157 (tt) REVERT: A 85 GLU cc_start: 0.9621 (mp0) cc_final: 0.9272 (pm20) REVERT: B 82 PHE cc_start: 0.8333 (m-80) cc_final: 0.7835 (m-80) REVERT: B 190 SER cc_start: 0.8834 (p) cc_final: 0.8221 (t) REVERT: B 241 MET cc_start: 0.3822 (tmm) cc_final: 0.2524 (ttt) REVERT: C 60 ASP cc_start: 0.8519 (m-30) cc_final: 0.8187 (m-30) REVERT: C 128 LEU cc_start: 0.9285 (pt) cc_final: 0.8978 (mm) REVERT: C 136 GLN cc_start: 0.8146 (tp40) cc_final: 0.7729 (tp40) REVERT: C 155 ILE cc_start: 0.8480 (pt) cc_final: 0.7920 (mt) REVERT: C 212 MET cc_start: 0.8312 (ptm) cc_final: 0.7484 (pmm) REVERT: C 280 MET cc_start: 0.8380 (mmp) cc_final: 0.6653 (tpp) REVERT: C 449 MET cc_start: 0.6944 (tmm) cc_final: 0.6577 (tpp) REVERT: D 172 LEU cc_start: 0.9602 (mm) cc_final: 0.9269 (mm) REVERT: D 178 ASN cc_start: 0.8604 (t0) cc_final: 0.8252 (t0) REVERT: D 308 PHE cc_start: 0.7971 (m-10) cc_final: 0.6996 (m-10) REVERT: D 487 HIS cc_start: 0.8850 (m90) cc_final: 0.8616 (m90) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2245 time to fit residues: 58.1676 Evaluate side-chains 144 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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: 5.9990 chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 147 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 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: 0.7090 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12261 Z= 0.325 Angle : 0.781 11.424 16660 Z= 0.389 Chirality : 0.047 0.331 1874 Planarity : 0.005 0.049 2122 Dihedral : 6.930 57.091 1774 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 33.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.07 % Allowed : 1.64 % 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: -1.59 (0.21), residues: 1468 helix: -0.81 (0.45), residues: 116 sheet: -0.47 (0.20), residues: 597 loop : -1.57 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 112 HIS 0.011 0.002 HIS B 105 PHE 0.027 0.002 PHE A 198 TYR 0.050 0.003 TYR A 124 ARG 0.009 0.001 ARG C 233 *********************** 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 169 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.510 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: 0.9456 (tt) cc_final: 0.9160 (tt) REVERT: A 85 GLU cc_start: 0.9695 (mp0) cc_final: 0.9345 (pm20) REVERT: A 129 MET cc_start: 0.9588 (mpp) cc_final: 0.9383 (mpp) REVERT: A 134 PHE cc_start: 0.9158 (m-10) cc_final: 0.8346 (m-80) REVERT: A 189 MET cc_start: 0.8848 (mmp) cc_final: 0.8619 (mmm) REVERT: A 201 ARG cc_start: 0.9392 (mmm160) cc_final: 0.9182 (tpt170) REVERT: B 82 PHE cc_start: 0.8510 (m-80) cc_final: 0.8102 (m-80) REVERT: B 190 SER cc_start: 0.9047 (p) cc_final: 0.8591 (t) REVERT: B 218 TYR cc_start: 0.9200 (t80) cc_final: 0.8653 (t80) REVERT: C 136 GLN cc_start: 0.8372 (tp40) cc_final: 0.7885 (tp40) REVERT: C 155 ILE cc_start: 0.8547 (pt) cc_final: 0.7994 (mt) REVERT: C 212 MET cc_start: 0.8369 (ptm) cc_final: 0.7793 (pmm) REVERT: C 280 MET cc_start: 0.8753 (mmp) cc_final: 0.6888 (tpt) REVERT: C 310 MET cc_start: 0.7869 (tmm) cc_final: 0.7564 (tmm) REVERT: D 172 LEU cc_start: 0.9553 (mm) cc_final: 0.9307 (mm) REVERT: D 487 HIS cc_start: 0.8846 (m90) cc_final: 0.8606 (m90) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2321 time to fit residues: 57.5777 Evaluate side-chains 130 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 0.3980 chunk 118 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 214 GLN ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 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: 0.6971 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12261 Z= 0.179 Angle : 0.690 9.905 16660 Z= 0.338 Chirality : 0.046 0.337 1874 Planarity : 0.005 0.048 2122 Dihedral : 6.494 57.347 1774 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % 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: -1.17 (0.21), residues: 1468 helix: 0.06 (0.48), residues: 109 sheet: -0.22 (0.21), residues: 585 loop : -1.33 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 398 HIS 0.009 0.001 HIS B 105 PHE 0.011 0.001 PHE C 122 TYR 0.020 0.002 TYR B 31 ARG 0.010 0.001 ARG B 317 ********************** 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 187 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.617 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 39 ASN cc_start: 0.9681 (m110) cc_final: 0.9460 (m-40) REVERT: A 66 ASP cc_start: 0.8682 (m-30) cc_final: 0.8271 (m-30) REVERT: A 85 GLU cc_start: 0.9688 (mp0) cc_final: 0.9325 (pm20) REVERT: A 134 PHE cc_start: 0.8943 (m-10) cc_final: 0.8117 (m-80) REVERT: B 82 PHE cc_start: 0.8128 (m-80) cc_final: 0.7711 (m-80) REVERT: B 136 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7209 (ttt-90) REVERT: B 190 SER cc_start: 0.8777 (p) cc_final: 0.8167 (t) REVERT: B 204 LEU cc_start: 0.9382 (mm) cc_final: 0.9002 (pt) REVERT: B 216 ASN cc_start: 0.9505 (m-40) cc_final: 0.9237 (m-40) REVERT: C 128 LEU cc_start: 0.9300 (pt) cc_final: 0.8994 (mm) REVERT: C 136 GLN cc_start: 0.8159 (tp40) cc_final: 0.7633 (tp40) REVERT: C 155 ILE cc_start: 0.8465 (pt) cc_final: 0.7910 (mt) REVERT: C 212 MET cc_start: 0.8617 (ptm) cc_final: 0.8033 (pmm) REVERT: C 280 MET cc_start: 0.8451 (mmp) cc_final: 0.6874 (tpp) REVERT: D 111 CYS cc_start: 0.8638 (t) cc_final: 0.8358 (t) REVERT: D 172 LEU cc_start: 0.9499 (mm) cc_final: 0.8783 (pp) REVERT: D 308 PHE cc_start: 0.8065 (m-10) cc_final: 0.7345 (m-10) REVERT: D 487 HIS cc_start: 0.8955 (m-70) cc_final: 0.8728 (m90) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2428 time to fit residues: 65.9581 Evaluate side-chains 141 residues out of total 1349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 C 111 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.100546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075918 restraints weight = 66288.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078198 restraints weight = 44309.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079784 restraints weight = 32677.169| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12261 Z= 0.212 Angle : 0.672 9.836 16660 Z= 0.333 Chirality : 0.045 0.347 1874 Planarity : 0.005 0.048 2122 Dihedral : 6.387 57.084 1774 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % 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 (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: -1.21 (0.21), residues: 1468 helix: -0.11 (0.47), residues: 110 sheet: -0.25 (0.20), residues: 598 loop : -1.35 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 112 HIS 0.005 0.001 HIS B 105 PHE 0.012 0.001 PHE A 198 TYR 0.017 0.002 TYR B 319 ARG 0.005 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.75 seconds wall clock time: 48 minutes 59.28 seconds (2939.28 seconds total)