Starting phenix.real_space_refine on Sun Dec 29 05:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpw_37725/12_2024/8wpw_37725_neut.cif" } resolution = 2.49 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= 0.001 sd= 0.018 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 38 5.16 5 C 6274 2.51 5 N 1654 2.21 5 O 1964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 9930 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1659 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 13, 'TRANS': 207} Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1619 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "R" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 14, 'TRANS': 180} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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 Time building chain proxies: 7.16, per 1000 atoms: 0.72 Number of scatterers: 9930 At special positions: 0 Unit cell: (86.7, 105.4, 171.7, 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 38 16.00 O 1964 8.00 N 1654 7.00 C 6274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN R 343 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 10.5% alpha, 45.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.009A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.975A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.701A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.774A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.950A pdb=" N THR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.886A pdb=" N GLN D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS D 127 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.734A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.757A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.217A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 371 Processing helix chain 'R' and resid 383 through 387 Processing helix chain 'R' and resid 405 through 410 removed outlier: 5.079A pdb=" N SER R 408 " --> pdb=" O ASN R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.759A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.100A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 removed outlier: 3.749A pdb=" N GLY A 153 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 removed outlier: 3.749A pdb=" N GLY A 153 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 removed outlier: 3.844A pdb=" N THR A 165 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 208 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS A 214 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.670A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.914A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 133 Processing sheet with id=AB3, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.867A pdb=" N LYS B 207 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.722A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.152A pdb=" N TYR C 33 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS C 95 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP C 109 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG C 97 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 126 through 129 removed outlier: 6.187A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 129 removed outlier: 6.187A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.586A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.369A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.369A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.722A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 133 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.757A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.110A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.837A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.837A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 93 through 94 Processing sheet with id=AD4, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'R' and resid 473 through 474 408 hydrogen bonds defined for protein. 978 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: 3.80 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3156 1.34 - 1.46: 2591 1.46 - 1.58: 4379 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 10174 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" CB PRO A 161 " pdb=" CG PRO A 161 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.79e+00 bond pdb=" C PRO D 94 " pdb=" N PRO D 95 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C5 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.19e+00 ... (remaining 10169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 13650 1.74 - 3.49: 173 3.49 - 5.23: 18 5.23 - 6.98: 3 6.98 - 8.72: 1 Bond angle restraints: 13845 Sorted by residual: angle pdb=" CA PRO A 161 " pdb=" N PRO A 161 " pdb=" CD PRO A 161 " ideal model delta sigma weight residual 112.00 107.02 4.98 1.40e+00 5.10e-01 1.26e+01 angle pdb=" N PRO A 161 " pdb=" CA PRO A 161 " pdb=" C PRO A 161 " ideal model delta sigma weight residual 112.47 117.25 -4.78 2.06e+00 2.36e-01 5.38e+00 angle pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.30e+00 angle pdb=" C ARG C 216 " pdb=" N VAL C 217 " pdb=" CA VAL C 217 " ideal model delta sigma weight residual 121.97 126.03 -4.06 1.80e+00 3.09e-01 5.08e+00 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.80 -4.26 1.91e+00 2.74e-01 4.98e+00 ... (remaining 13840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.58: 5676 13.58 - 27.15: 297 27.15 - 40.73: 80 40.73 - 54.31: 19 54.31 - 67.89: 6 Dihedral angle restraints: 6078 sinusoidal: 2346 harmonic: 3732 Sorted by residual: dihedral pdb=" CA PHE A 160 " pdb=" C PHE A 160 " pdb=" N PRO A 161 " pdb=" CA PRO A 161 " ideal model delta harmonic sigma weight residual -180.00 -138.60 -41.40 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLU C 154 " pdb=" C GLU C 154 " pdb=" N PRO C 155 " pdb=" CA PRO C 155 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TRP R 353 " pdb=" C TRP R 353 " pdb=" N ASN R 354 " pdb=" CA ASN R 354 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1174 0.042 - 0.085: 239 0.085 - 0.127: 123 0.127 - 0.170: 6 0.170 - 0.212: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CA PRO A 161 " pdb=" N PRO A 161 " pdb=" C PRO A 161 " pdb=" CB PRO A 161 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL C 217 " pdb=" CA VAL C 217 " pdb=" CG1 VAL C 217 " pdb=" CG2 VAL C 217 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA PHE C 152 " pdb=" N PHE C 152 " pdb=" C PHE C 152 " pdb=" CB PHE C 152 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1540 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 160 " -0.095 5.00e-02 4.00e+02 1.44e-01 3.32e+01 pdb=" N PRO A 161 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 52 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 53 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 154 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO C 155 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 155 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 155 " 0.019 5.00e-02 4.00e+02 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 124 2.68 - 3.24: 8765 3.24 - 3.79: 14223 3.79 - 4.35: 19691 4.35 - 4.90: 34190 Nonbonded interactions: 76993 Sorted by model distance: nonbonded pdb=" NE ARG A 38 " pdb=" OE2 GLU A 46 " model vdw 2.131 3.120 nonbonded pdb=" O THR R 393 " pdb=" OG1 THR R 523 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP D 171 " pdb=" OG1 THR D 173 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 172 " model vdw 2.282 3.040 nonbonded pdb=" O PRO A 199 " pdb=" OG SER A 202 " model vdw 2.293 3.040 ... (remaining 76988 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 individual isotropic 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 28.310 Find NCS groups from input model: 0.210 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.003 0.067 10174 Z= 0.177 Angle : 0.503 8.720 13845 Z= 0.258 Chirality : 0.042 0.212 1543 Planarity : 0.005 0.144 1772 Dihedral : 9.267 67.887 3666 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 1.63 % Allowed : 4.08 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.00 (0.24), residues: 1280 helix: -2.51 (0.72), residues: 39 sheet: 0.73 (0.23), residues: 534 loop : -0.38 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 109 HIS 0.003 0.001 HIS B 92 PHE 0.011 0.001 PHE C 27 TYR 0.012 0.001 TYR C 33 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.175 Fit side-chains REVERT: A 194 SER cc_start: 0.8549 (t) cc_final: 0.8267 (m) REVERT: A 212 VAL cc_start: 0.7923 (t) cc_final: 0.7697 (m) REVERT: B 83 ASP cc_start: 0.7559 (m-30) cc_final: 0.6956 (m-30) REVERT: B 105 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6707 (mt-10) REVERT: B 141 PRO cc_start: 0.6244 (Cg_exo) cc_final: 0.6014 (Cg_endo) REVERT: C 31 TYR cc_start: 0.8478 (m-10) cc_final: 0.8241 (m-10) REVERT: D 90 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (pp30) REVERT: D 163 SER cc_start: 0.8047 (t) cc_final: 0.7847 (p) REVERT: D 164 VAL cc_start: 0.8240 (t) cc_final: 0.7989 (p) REVERT: H 112 GLN cc_start: 0.6895 (mp10) cc_final: 0.6618 (mp10) REVERT: L 108 LYS cc_start: 0.8042 (pttm) cc_final: 0.7467 (mmtt) REVERT: R 420 ASP cc_start: 0.7811 (m-30) cc_final: 0.7587 (m-30) REVERT: R 460 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8526 (mtmt) outliers start: 18 outliers final: 5 residues processed: 271 average time/residue: 0.7956 time to fit residues: 240.1200 Evaluate side-chains 219 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 213 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS C 39 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10174 Z= 0.175 Angle : 0.581 8.994 13845 Z= 0.299 Chirality : 0.044 0.213 1543 Planarity : 0.006 0.145 1772 Dihedral : 4.977 41.279 1476 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.36 % Favored : 96.48 % Rotamer: Outliers : 3.36 % Allowed : 10.80 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.09 (0.24), residues: 1280 helix: -2.14 (0.76), residues: 41 sheet: 0.82 (0.23), residues: 557 loop : -0.41 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS B 189 PHE 0.024 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.106 Fit side-chains REVERT: A 119 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 82 GLU cc_start: 0.6732 (pm20) cc_final: 0.6437 (pm20) REVERT: B 141 PRO cc_start: 0.6311 (Cg_exo) cc_final: 0.6083 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (pp30) REVERT: H 4 LEU cc_start: 0.8759 (mt) cc_final: 0.8366 (mt) REVERT: H 112 GLN cc_start: 0.6930 (mp10) cc_final: 0.6629 (mp10) REVERT: R 335 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7768 (mp) REVERT: R 403 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7320 (ptp-170) REVERT: R 420 ASP cc_start: 0.7786 (m-30) cc_final: 0.7545 (m-30) REVERT: R 460 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8457 (mtmt) outliers start: 37 outliers final: 15 residues processed: 216 average time/residue: 0.9113 time to fit residues: 216.8073 Evaluate side-chains 203 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10174 Z= 0.274 Angle : 0.603 10.780 13845 Z= 0.308 Chirality : 0.045 0.218 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.032 41.621 1473 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 12.34 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.05 (0.24), residues: 1280 helix: -1.95 (0.80), residues: 41 sheet: 0.79 (0.22), residues: 556 loop : -0.45 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.021 0.002 PHE C 27 TYR 0.017 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 1.113 Fit side-chains REVERT: A 119 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: B 141 PRO cc_start: 0.6416 (Cg_exo) cc_final: 0.6206 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (pp30) REVERT: D 164 VAL cc_start: 0.8356 (t) cc_final: 0.8126 (p) REVERT: H 4 LEU cc_start: 0.8774 (mt) cc_final: 0.8376 (mt) REVERT: H 112 GLN cc_start: 0.6937 (mp10) cc_final: 0.6640 (mp10) REVERT: R 335 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7811 (mp) REVERT: R 357 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7447 (ttp80) REVERT: R 403 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7295 (ptp-170) REVERT: R 420 ASP cc_start: 0.7800 (m-30) cc_final: 0.7585 (m-30) REVERT: R 460 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8542 (mtmt) outliers start: 42 outliers final: 22 residues processed: 219 average time/residue: 0.9041 time to fit residues: 217.4640 Evaluate side-chains 224 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 481 ASN Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10174 Z= 0.186 Angle : 0.568 8.979 13845 Z= 0.288 Chirality : 0.043 0.211 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.916 41.032 1473 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 3.18 % Allowed : 13.61 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.06 (0.23), residues: 1280 helix: -1.79 (0.82), residues: 41 sheet: 0.77 (0.22), residues: 557 loop : -0.43 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.209 Fit side-chains REVERT: A 119 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: A 177 VAL cc_start: 0.8339 (t) cc_final: 0.8126 (p) REVERT: B 141 PRO cc_start: 0.6382 (Cg_exo) cc_final: 0.6182 (Cg_endo) REVERT: B 146 VAL cc_start: 0.7648 (m) cc_final: 0.7444 (t) REVERT: D 90 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8285 (pp30) REVERT: D 164 VAL cc_start: 0.8340 (t) cc_final: 0.8102 (p) REVERT: R 335 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7793 (mp) REVERT: R 357 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7386 (ttp80) REVERT: R 403 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7284 (ptp-170) REVERT: R 420 ASP cc_start: 0.7782 (m-30) cc_final: 0.7557 (m-30) REVERT: R 460 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8527 (mtmt) outliers start: 35 outliers final: 22 residues processed: 217 average time/residue: 0.9090 time to fit residues: 216.6810 Evaluate side-chains 216 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 109 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 76 ASN C 170 HIS D 6 GLN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10174 Z= 0.218 Angle : 0.575 8.969 13845 Z= 0.292 Chirality : 0.043 0.215 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.923 41.361 1473 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 3.81 % Allowed : 13.43 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.06 (0.23), residues: 1280 helix: -1.74 (0.82), residues: 41 sheet: 0.81 (0.22), residues: 554 loop : -0.46 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.194 Fit side-chains REVERT: A 119 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: A 177 VAL cc_start: 0.8374 (t) cc_final: 0.8153 (p) REVERT: B 170 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6689 (p0) REVERT: D 90 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8275 (pp30) REVERT: D 164 VAL cc_start: 0.8346 (t) cc_final: 0.8116 (p) REVERT: R 335 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7820 (mp) REVERT: R 357 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7386 (ttp80) REVERT: R 403 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7226 (ptp-170) REVERT: R 420 ASP cc_start: 0.7794 (m-30) cc_final: 0.7570 (m-30) REVERT: R 460 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8553 (mtmt) outliers start: 42 outliers final: 32 residues processed: 219 average time/residue: 0.9233 time to fit residues: 222.0749 Evaluate side-chains 230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10174 Z= 0.236 Angle : 0.591 11.259 13845 Z= 0.298 Chirality : 0.044 0.214 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.955 41.351 1473 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 3.81 % Allowed : 14.16 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.05 (0.23), residues: 1280 helix: -1.71 (0.83), residues: 41 sheet: 0.83 (0.22), residues: 554 loop : -0.50 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 1.095 Fit side-chains REVERT: A 119 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: A 177 VAL cc_start: 0.8384 (t) cc_final: 0.8162 (p) REVERT: B 172 THR cc_start: 0.8233 (p) cc_final: 0.7993 (t) REVERT: D 90 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (pp30) REVERT: D 164 VAL cc_start: 0.8363 (t) cc_final: 0.8142 (p) REVERT: H 112 GLN cc_start: 0.6802 (mp10) cc_final: 0.6521 (mp10) REVERT: R 335 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (mp) REVERT: R 357 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7376 (ttp80) REVERT: R 403 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7175 (ptp-170) REVERT: R 420 ASP cc_start: 0.7792 (m-30) cc_final: 0.7571 (m-30) REVERT: R 460 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8577 (mtmt) outliers start: 42 outliers final: 33 residues processed: 226 average time/residue: 0.8887 time to fit residues: 221.1521 Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10174 Z= 0.253 Angle : 0.597 10.238 13845 Z= 0.304 Chirality : 0.044 0.213 1543 Planarity : 0.005 0.145 1772 Dihedral : 5.000 41.597 1473 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 4.08 % Allowed : 14.07 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.02 (0.23), residues: 1280 helix: -1.72 (0.83), residues: 41 sheet: 0.81 (0.22), residues: 555 loop : -0.52 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.016 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 1.171 Fit side-chains REVERT: A 119 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: A 177 VAL cc_start: 0.8414 (t) cc_final: 0.8190 (p) REVERT: D 90 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8277 (pp30) REVERT: H 38 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7002 (ptp-170) REVERT: H 112 GLN cc_start: 0.6825 (mp10) cc_final: 0.6581 (mp10) REVERT: R 335 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7846 (mp) REVERT: R 357 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7400 (ttp80) REVERT: R 403 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7169 (ptp-170) REVERT: R 420 ASP cc_start: 0.7790 (m-30) cc_final: 0.7560 (m-30) REVERT: R 460 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8568 (mtmt) outliers start: 45 outliers final: 33 residues processed: 221 average time/residue: 0.9050 time to fit residues: 219.4320 Evaluate side-chains 234 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.0060 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10174 Z= 0.230 Angle : 0.593 9.843 13845 Z= 0.300 Chirality : 0.044 0.210 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.976 41.283 1473 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.63 % Allowed : 14.79 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.03 (0.23), residues: 1280 helix: -1.68 (0.83), residues: 41 sheet: 0.81 (0.22), residues: 555 loop : -0.52 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 1.142 Fit side-chains REVERT: A 119 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: A 177 VAL cc_start: 0.8403 (t) cc_final: 0.8181 (p) REVERT: H 112 GLN cc_start: 0.6800 (mp10) cc_final: 0.6561 (mp10) REVERT: R 357 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7402 (ttp80) REVERT: R 386 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8170 (mptt) REVERT: R 403 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7174 (ptp-170) REVERT: R 420 ASP cc_start: 0.7787 (m-30) cc_final: 0.7563 (m-30) REVERT: R 460 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8586 (mtmt) outliers start: 40 outliers final: 32 residues processed: 219 average time/residue: 0.8833 time to fit residues: 213.2458 Evaluate side-chains 232 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 112 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10174 Z= 0.211 Angle : 0.585 9.556 13845 Z= 0.297 Chirality : 0.044 0.210 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.701 40.993 1470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 3.54 % Allowed : 14.97 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.06 (0.23), residues: 1280 helix: -1.64 (0.84), residues: 41 sheet: 0.83 (0.22), residues: 555 loop : -0.49 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.003 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 1.127 Fit side-chains REVERT: A 119 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 177 VAL cc_start: 0.8394 (t) cc_final: 0.8173 (p) REVERT: D 90 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (pp30) REVERT: H 38 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7009 (ptp-170) REVERT: H 112 GLN cc_start: 0.6795 (mp10) cc_final: 0.6561 (mp10) REVERT: R 357 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7405 (ttp80) REVERT: R 386 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8186 (mptt) REVERT: R 403 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7175 (ptp-170) REVERT: R 420 ASP cc_start: 0.7770 (m-30) cc_final: 0.7541 (m-30) REVERT: R 460 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8581 (mtmt) outliers start: 39 outliers final: 31 residues processed: 213 average time/residue: 0.9095 time to fit residues: 212.6317 Evaluate side-chains 231 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.0010 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10174 Z= 0.222 Angle : 0.594 9.420 13845 Z= 0.301 Chirality : 0.044 0.212 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.708 40.828 1470 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 3.54 % Allowed : 14.97 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.06 (0.23), residues: 1280 helix: -1.67 (0.83), residues: 41 sheet: 0.84 (0.22), residues: 554 loop : -0.51 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.004 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 1.191 Fit side-chains REVERT: A 119 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: A 177 VAL cc_start: 0.8402 (t) cc_final: 0.8178 (p) REVERT: D 90 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8269 (pp30) REVERT: H 38 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7011 (ptp-170) REVERT: R 357 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: R 386 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8191 (mptt) REVERT: R 403 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7173 (ptp-170) REVERT: R 420 ASP cc_start: 0.7766 (m-30) cc_final: 0.7537 (m-30) REVERT: R 460 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8582 (mtmt) outliers start: 39 outliers final: 30 residues processed: 214 average time/residue: 0.9515 time to fit residues: 224.8698 Evaluate side-chains 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Chi-restraints excluded: chain R residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110587 restraints weight = 14060.843| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.89 r_work: 0.3393 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10174 Z= 0.225 Angle : 0.597 9.277 13845 Z= 0.302 Chirality : 0.044 0.212 1543 Planarity : 0.005 0.146 1772 Dihedral : 4.721 40.732 1470 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.27 % Allowed : 15.15 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: 0.06 (0.23), residues: 1280 helix: -1.68 (0.83), residues: 41 sheet: 0.84 (0.22), residues: 554 loop : -0.51 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 353 HIS 0.004 0.001 HIS B 92 PHE 0.021 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.004 0.000 ARG R 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4245.01 seconds wall clock time: 77 minutes 10.06 seconds (4630.06 seconds total)