Starting phenix.real_space_refine on Fri Feb 14 07:24:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpw_37725/02_2025/8wpw_37725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpw_37725/02_2025/8wpw_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_37725/02_2025/8wpw_37725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpw_37725/02_2025/8wpw_37725.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpw_37725/02_2025/8wpw_37725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpw_37725/02_2025/8wpw_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-5592/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: 6.30, per 1000 atoms: 0.63 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 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: 1.62 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: 3.48 Time building geometry restraints manager: 2.82 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: 3.200 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.380 Find NCS groups from input model: 0.180 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- 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 : 1.091 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: 0.7699 time to fit residues: 231.7858 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 : 1.082 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110561 restraints weight = 13981.225| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.89 r_work: 0.3406 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.990 Fit side-chains REVERT: A 119 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: A 223 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7303 (tttt) REVERT: B 82 GLU cc_start: 0.7142 (pm20) cc_final: 0.6841 (pm20) REVERT: B 141 PRO cc_start: 0.6622 (Cg_exo) cc_final: 0.6408 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8402 (pp30) REVERT: H 4 LEU cc_start: 0.8847 (mt) cc_final: 0.8509 (mt) REVERT: H 112 GLN cc_start: 0.7649 (mp10) cc_final: 0.7325 (mp10) REVERT: R 335 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7949 (mp) REVERT: R 403 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7547 (ptp-170) REVERT: R 420 ASP cc_start: 0.8108 (m-30) cc_final: 0.7895 (m-30) REVERT: R 460 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8618 (mtmt) outliers start: 37 outliers final: 15 residues processed: 216 average time/residue: 0.9025 time to fit residues: 214.6555 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 : 1.068 ------------------------------------------------------------------------------- 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 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.0020 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110185 restraints weight = 14305.589| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.90 r_work: 0.3399 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1454 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= 0.190 Angle : 0.570 10.666 13845 Z= 0.290 Chirality : 0.043 0.214 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.881 40.876 1473 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 3.36 % Allowed : 12.52 % Favored : 84.12 % 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: 0.11 (0.24), residues: 1280 helix: -1.90 (0.80), residues: 41 sheet: 0.81 (0.23), residues: 556 loop : -0.40 (0.23), residues: 683 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 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 228 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.034 Fit side-chains REVERT: A 119 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: A 223 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7322 (tttt) REVERT: D 90 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (pp30) REVERT: D 164 VAL cc_start: 0.8548 (t) cc_final: 0.8317 (p) REVERT: R 357 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8053 (ttp80) REVERT: R 403 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7535 (ptp-170) REVERT: R 460 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8663 (mtmt) outliers start: 37 outliers final: 20 residues processed: 210 average time/residue: 0.9447 time to fit residues: 217.3475 Evaluate side-chains 212 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL 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 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 350 VAL Chi-restraints excluded: chain R residue 356 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 8.9990 chunk 121 optimal weight: 0.0270 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108934 restraints weight = 14005.050| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.89 r_work: 0.3373 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10174 Z= 0.341 Angle : 0.628 9.022 13845 Z= 0.321 Chirality : 0.046 0.220 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.148 42.201 1473 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 3.72 % Allowed : 12.98 % Favored : 83.30 % 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: -0.01 (0.23), residues: 1280 helix: -1.88 (0.82), residues: 41 sheet: 0.76 (0.22), residues: 557 loop : -0.51 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 47 HIS 0.005 0.001 HIS B 92 PHE 0.021 0.002 PHE C 27 TYR 0.019 0.002 TYR C 33 ARG 0.004 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 244 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.996 Fit side-chains REVERT: A 119 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: A 177 VAL cc_start: 0.8439 (t) cc_final: 0.8217 (p) REVERT: A 223 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7322 (tttt) REVERT: D 90 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8448 (pp30) REVERT: D 164 VAL cc_start: 0.8530 (t) cc_final: 0.8298 (p) REVERT: H 112 GLN cc_start: 0.7557 (mp10) cc_final: 0.7231 (mp10) REVERT: R 335 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8012 (mp) REVERT: R 357 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8032 (ttp80) REVERT: R 403 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7436 (ptp-170) outliers start: 41 outliers final: 27 residues processed: 225 average time/residue: 0.8979 time to fit residues: 221.7490 Evaluate side-chains 230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 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 9 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 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 6 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 34 ASN ** D 159 ASN ** 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 = 0.3876 r_free = 0.3876 target = 0.135714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109979 restraints weight = 14080.834| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.88 r_work: 0.3386 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1651 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= 0.223 Angle : 0.593 11.538 13845 Z= 0.299 Chirality : 0.044 0.211 1543 Planarity : 0.005 0.145 1772 Dihedral : 5.041 41.689 1473 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 13.97 % Favored : 82.67 % 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 (0.23), residues: 1280 helix: -1.89 (0.81), residues: 41 sheet: 0.80 (0.22), residues: 554 loop : -0.52 (0.23), residues: 685 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 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 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 1.132 Fit side-chains REVERT: A 119 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: A 177 VAL cc_start: 0.8417 (t) cc_final: 0.8188 (p) REVERT: A 223 LYS cc_start: 0.7578 (ttmm) cc_final: 0.7311 (tttt) REVERT: D 90 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8440 (pp30) REVERT: D 164 VAL cc_start: 0.8522 (t) cc_final: 0.8299 (p) REVERT: H 112 GLN cc_start: 0.7503 (mp10) cc_final: 0.7183 (mp10) REVERT: R 335 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (mp) REVERT: R 357 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8022 (ttp80) REVERT: R 403 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7421 (ptp-170) outliers start: 37 outliers final: 25 residues processed: 215 average time/residue: 0.9388 time to fit residues: 221.4540 Evaluate side-chains 218 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 52 SER 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 H residue 7 SER Chi-restraints excluded: chain H residue 25 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 18 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.0020 chunk 79 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110815 restraints weight = 14166.774| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.89 r_work: 0.3407 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1797 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= 0.160 Angle : 0.557 9.700 13845 Z= 0.280 Chirality : 0.043 0.209 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.816 40.863 1473 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 3.54 % Allowed : 14.43 % 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: 0.10 (0.24), residues: 1280 helix: -1.79 (0.81), residues: 41 sheet: 0.85 (0.22), residues: 554 loop : -0.45 (0.23), residues: 685 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 0.012 0.001 TYR C 33 ARG 0.003 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 236 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.138 Fit side-chains REVERT: A 119 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: A 177 VAL cc_start: 0.8376 (t) cc_final: 0.8147 (p) REVERT: A 223 LYS cc_start: 0.7541 (ttmm) cc_final: 0.7275 (tttt) REVERT: B 146 VAL cc_start: 0.7879 (m) cc_final: 0.7659 (t) REVERT: B 170 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7038 (p0) REVERT: D 164 VAL cc_start: 0.8539 (t) cc_final: 0.8317 (p) REVERT: R 335 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7998 (mp) REVERT: R 357 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7991 (ttp80) REVERT: R 366 SER cc_start: 0.8493 (p) cc_final: 0.8291 (m) REVERT: R 386 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (mptt) REVERT: R 403 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7463 (ptp-170) outliers start: 39 outliers final: 29 residues processed: 219 average time/residue: 0.8821 time to fit residues: 213.7375 Evaluate side-chains 227 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 20 THR Chi-restraints excluded: chain D residue 52 SER 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 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 18 ARG 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 123 optimal weight: 0.0020 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110327 restraints weight = 14282.801| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.90 r_work: 0.3399 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1847 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= 0.200 Angle : 0.569 9.040 13845 Z= 0.288 Chirality : 0.043 0.213 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.609 40.746 1470 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.33 % Rotamer: Outliers : 3.54 % Allowed : 14.61 % 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: 0.07 (0.23), residues: 1280 helix: -1.75 (0.81), residues: 41 sheet: 0.81 (0.22), residues: 558 loop : -0.46 (0.23), residues: 681 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 0.020 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.003 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 236 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.014 Fit side-chains REVERT: A 119 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 177 VAL cc_start: 0.8389 (t) cc_final: 0.8163 (p) REVERT: A 223 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7268 (tttt) REVERT: B 146 VAL cc_start: 0.7879 (m) cc_final: 0.7657 (t) REVERT: B 170 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7059 (p0) REVERT: D 90 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8450 (pp30) REVERT: D 164 VAL cc_start: 0.8555 (t) cc_final: 0.8342 (p) REVERT: R 335 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8014 (mp) REVERT: R 357 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7995 (ttp80) REVERT: R 386 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8302 (mptt) REVERT: R 403 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7472 (ptp-170) outliers start: 39 outliers final: 29 residues processed: 216 average time/residue: 0.8723 time to fit residues: 207.4289 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 : 1.127 ------------------------------------------------------------------------------- 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 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 52 SER 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 62 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.110101 restraints weight = 14170.818| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.90 r_work: 0.3391 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1866 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 : 0.589 8.856 13845 Z= 0.299 Chirality : 0.044 0.213 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.690 40.993 1470 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 4.08 % Allowed : 14.52 % Favored : 81.40 % 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: 0.07 (0.23), residues: 1280 helix: -1.77 (0.81), residues: 41 sheet: 0.85 (0.22), residues: 555 loop : -0.50 (0.23), residues: 684 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 0.015 0.001 TYR C 33 ARG 0.004 0.000 ARG A 38 *********************** 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 242 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 1.072 Fit side-chains REVERT: A 119 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: A 177 VAL cc_start: 0.8407 (t) cc_final: 0.8192 (p) REVERT: A 223 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7256 (tttt) REVERT: B 146 VAL cc_start: 0.7890 (m) cc_final: 0.7673 (t) REVERT: D 90 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8452 (pp30) REVERT: D 171 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7044 (p0) REVERT: H 38 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7243 (ptp-170) REVERT: R 335 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8021 (mp) REVERT: R 357 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8008 (ttp80) REVERT: R 386 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8321 (mptt) REVERT: R 403 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7422 (ptp-170) outliers start: 45 outliers final: 30 residues processed: 222 average time/residue: 0.9042 time to fit residues: 220.3378 Evaluate side-chains 235 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 165 GLU 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 D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER 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 171 ASP 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 L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG 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 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 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 107 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109029 restraints weight = 14214.567| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.89 r_work: 0.3382 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10174 Z= 0.279 Angle : 0.612 8.890 13845 Z= 0.311 Chirality : 0.045 0.215 1543 Planarity : 0.006 0.145 1772 Dihedral : 4.807 41.328 1470 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 3.72 % Allowed : 15.25 % Favored : 81.03 % 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: 0.03 (0.23), residues: 1280 helix: -1.81 (0.81), residues: 41 sheet: 0.85 (0.22), residues: 554 loop : -0.54 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.004 0.001 HIS B 92 PHE 0.020 0.002 PHE C 27 TYR 0.016 0.001 TYR C 33 ARG 0.004 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 241 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.070 Fit side-chains REVERT: A 119 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: A 177 VAL cc_start: 0.8422 (t) cc_final: 0.8207 (p) REVERT: A 223 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7245 (tttt) REVERT: B 146 VAL cc_start: 0.7904 (m) cc_final: 0.7684 (t) REVERT: B 178 THR cc_start: 0.8555 (m) cc_final: 0.8239 (t) REVERT: D 90 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: D 171 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7099 (p0) REVERT: H 38 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7250 (ptp-170) REVERT: H 112 GLN cc_start: 0.7473 (mp10) cc_final: 0.7198 (mp10) REVERT: R 335 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8035 (mp) REVERT: R 357 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8026 (ttp80) REVERT: R 386 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8333 (mptt) REVERT: R 403 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7413 (ptp-170) outliers start: 41 outliers final: 31 residues processed: 220 average time/residue: 0.9300 time to fit residues: 224.1496 Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER 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 171 ASP 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 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 18 ARG 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 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 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.108993 restraints weight = 14212.344| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10174 Z= 0.294 Angle : 0.635 12.241 13845 Z= 0.319 Chirality : 0.045 0.215 1543 Planarity : 0.006 0.145 1772 Dihedral : 4.840 41.358 1470 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 3.36 % Allowed : 15.88 % Favored : 80.76 % 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: 0.01 (0.23), residues: 1280 helix: -1.82 (0.81), residues: 41 sheet: 0.83 (0.22), residues: 554 loop : -0.56 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 109 HIS 0.005 0.001 HIS B 92 PHE 0.021 0.002 PHE C 27 TYR 0.017 0.002 TYR C 33 ARG 0.004 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 231 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.160 Fit side-chains REVERT: A 119 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: A 177 VAL cc_start: 0.8426 (t) cc_final: 0.8212 (p) REVERT: B 178 THR cc_start: 0.8565 (m) cc_final: 0.8245 (t) REVERT: D 90 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (pp30) REVERT: D 171 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7108 (p0) REVERT: H 38 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7255 (ptp-170) REVERT: H 112 GLN cc_start: 0.7491 (mp10) cc_final: 0.7219 (mp10) REVERT: R 335 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8034 (mp) REVERT: R 357 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8037 (ttp80) REVERT: R 386 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8340 (mptt) REVERT: R 403 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7425 (ptp-170) outliers start: 37 outliers final: 29 residues processed: 214 average time/residue: 0.9901 time to fit residues: 233.0418 Evaluate side-chains 230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER 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 171 ASP 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 L residue 18 ARG 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 356 LYS Chi-restraints excluded: chain R residue 357 ARG 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 3 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110081 restraints weight = 14084.136| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.89 r_work: 0.3389 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1940 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= 0.234 Angle : 0.608 12.024 13845 Z= 0.307 Chirality : 0.044 0.210 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.770 40.988 1470 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 3.63 % Allowed : 15.70 % Favored : 80.67 % 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: -1.77 (0.81), residues: 41 sheet: 0.83 (0.22), residues: 554 loop : -0.52 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 353 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 0.003 0.000 ARG R 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9304.87 seconds wall clock time: 164 minutes 27.86 seconds (9867.86 seconds total)