Starting phenix.real_space_refine on Wed Aug 5 12:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_37725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_37725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_37725_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_37725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpw_37725/08_2026/8wpw_37725.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 1.82, per 1000 atoms: 0.18 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: 0.90 Conformation dependent library (CDL) restraints added in 359.0 milliseconds 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: 0.23 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: 1.53 Time building geometry restraints manager: 1.19 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: 3.580 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.050 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 10191 Z= 0.118 Angle : 0.506 8.720 13882 Z= 0.259 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 : 4.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG H 38 TYR 0.012 0.001 TYR C 33 PHE 0.011 0.001 PHE C 27 TRP 0.010 0.001 TRP C 109 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10174) covalent geometry : angle 0.50323 / 0.26 (13845) SS BOND : bond 0.00430 / 0.26 ( 14) SS BOND : angle 0.75558 / 0.54 ( 28) hydrogen bonds : bond 0.24702 / 16.90 ( 357) hydrogen bonds : angle 9.28094 / 6.40 ( 978) link_BETA1-4 : bond 0.00195 / 0.10 ( 1) link_BETA1-4 : angle 1.66434 / 0.87 ( 3) link_BETA1-6 : bond 0.00173 / 0.09 ( 1) link_BETA1-6 : angle 1.72208 / 0.95 ( 3) link_NAG-ASN : bond 0.00281 / 0.15 ( 1) link_NAG-ASN : angle 1.89634 / 1.09 ( 3) *********************** 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 : 0.271 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: 0.6957 (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: 0.2971 time to fit residues: 90.0501 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 : 0.310 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109794 restraints weight = 14114.913| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.88 r_work: 0.3395 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10191 Z= 0.141 Angle : 0.597 9.002 13882 Z= 0.308 Chirality : 0.044 0.214 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.029 41.273 1476 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 3.36 % Allowed : 10.71 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1280 helix: -2.14 (0.77), residues: 41 sheet: 0.79 (0.23), residues: 562 loop : -0.43 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.015 0.001 TYR C 33 PHE 0.022 0.001 PHE C 27 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10174) covalent geometry : angle 0.59288 / 0.31 (13845) SS BOND : bond 0.00702 / 0.40 ( 14) SS BOND : angle 1.52539 / 1.14 ( 28) hydrogen bonds : bond 0.04499 / 3.04 ( 357) hydrogen bonds : angle 6.34971 / 4.37 ( 978) link_BETA1-4 : bond 0.00095 / 0.05 ( 1) link_BETA1-4 : angle 1.65661 / 0.87 ( 3) link_BETA1-6 : bond 0.00033 / 0.02 ( 1) link_BETA1-6 : angle 1.70658 / 0.92 ( 3) link_NAG-ASN : bond 0.00437 / 0.23 ( 1) link_NAG-ASN : angle 1.31388 / 0.75 ( 3) *********************** 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 243 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.254 Fit side-chains REVERT: A 119 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: A 223 LYS cc_start: 0.7522 (ttmm) cc_final: 0.7310 (tttt) REVERT: B 141 PRO cc_start: 0.6663 (Cg_exo) cc_final: 0.6453 (Cg_endo) REVERT: B 197 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7828 (p) REVERT: D 90 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8412 (pp30) REVERT: H 4 LEU cc_start: 0.8850 (mt) cc_final: 0.8508 (mt) REVERT: H 112 GLN cc_start: 0.7666 (mp10) cc_final: 0.7349 (mp10) REVERT: R 335 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7954 (mp) REVERT: R 403 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7543 (ptp-170) REVERT: R 420 ASP cc_start: 0.8113 (m-30) cc_final: 0.7907 (m-30) REVERT: R 460 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8639 (mtmt) outliers start: 37 outliers final: 16 residues processed: 225 average time/residue: 0.3442 time to fit residues: 85.6274 Evaluate side-chains 209 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 11 LEU 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 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 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 16 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108390 restraints weight = 14190.779| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.88 r_work: 0.3374 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10191 Z= 0.205 Angle : 0.627 10.606 13882 Z= 0.321 Chirality : 0.046 0.219 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.136 42.188 1473 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 3.99 % Allowed : 12.52 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1280 helix: -2.00 (0.80), residues: 41 sheet: 0.77 (0.22), residues: 561 loop : -0.53 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.019 0.002 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.012 0.002 TRP A 47 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (10174) covalent geometry : angle 0.62097 / 0.32 (13845) SS BOND : bond 0.00833 / 0.51 ( 14) SS BOND : angle 1.74889 / 1.29 ( 28) hydrogen bonds : bond 0.04309 / 2.92 ( 357) hydrogen bonds : angle 5.92119 / 4.05 ( 978) link_BETA1-4 : bond 0.00295 / 0.16 ( 1) link_BETA1-4 : angle 1.80036 / 0.95 ( 3) link_BETA1-6 : bond 0.00089 / 0.05 ( 1) link_BETA1-6 : angle 1.45296 / 0.79 ( 3) link_NAG-ASN : bond 0.00340 / 0.18 ( 1) link_NAG-ASN : angle 2.11630 / 1.19 ( 3) *********************** 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 249 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.376 Fit side-chains REVERT: A 119 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: A 177 VAL cc_start: 0.8409 (t) cc_final: 0.8201 (p) REVERT: A 223 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7348 (tttt) REVERT: B 197 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7803 (p) REVERT: D 90 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (pp30) REVERT: D 164 VAL cc_start: 0.8537 (t) cc_final: 0.8308 (p) REVERT: H 4 LEU cc_start: 0.8874 (mt) cc_final: 0.8554 (mt) REVERT: H 112 GLN cc_start: 0.7571 (mp10) cc_final: 0.7262 (mp10) REVERT: R 335 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8004 (mp) REVERT: R 357 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8061 (ttp80) REVERT: R 403 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7492 (ptp-170) REVERT: R 460 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8693 (mtmt) outliers start: 44 outliers final: 23 residues processed: 226 average time/residue: 0.3046 time to fit residues: 76.0908 Evaluate side-chains 228 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU 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 30 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 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 481 ASN Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 123 optimal weight: 0.0030 chunk 105 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN B 160 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108584 restraints weight = 14363.854| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.91 r_work: 0.3372 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10191 Z= 0.179 Angle : 0.621 10.999 13882 Z= 0.315 Chirality : 0.045 0.214 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.160 42.222 1473 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.54 % Allowed : 13.43 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1280 helix: -1.94 (0.81), residues: 41 sheet: 0.76 (0.22), residues: 556 loop : -0.56 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.016 0.001 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (10174) covalent geometry : angle 0.61486 / 0.31 (13845) SS BOND : bond 0.00722 / 0.43 ( 14) SS BOND : angle 1.80469 / 1.37 ( 28) hydrogen bonds : bond 0.03867 / 2.62 ( 357) hydrogen bonds : angle 5.65757 / 3.86 ( 978) link_BETA1-4 : bond 0.00262 / 0.14 ( 1) link_BETA1-4 : angle 1.60397 / 0.85 ( 3) link_BETA1-6 : bond 0.00182 / 0.10 ( 1) link_BETA1-6 : angle 1.38296 / 0.76 ( 3) link_NAG-ASN : bond 0.00374 / 0.20 ( 1) link_NAG-ASN : angle 1.98787 / 1.12 ( 3) *********************** 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 242 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.307 Fit side-chains REVERT: A 119 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: A 177 VAL cc_start: 0.8441 (t) cc_final: 0.8220 (p) REVERT: A 223 LYS cc_start: 0.7574 (ttmm) cc_final: 0.7330 (tttt) REVERT: B 170 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6998 (p0) REVERT: D 90 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8448 (pp30) REVERT: D 164 VAL cc_start: 0.8532 (t) cc_final: 0.8300 (p) REVERT: H 4 LEU cc_start: 0.8897 (mt) cc_final: 0.8549 (mt) REVERT: H 112 GLN cc_start: 0.7566 (mp10) cc_final: 0.7235 (mp10) REVERT: R 335 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8010 (mp) REVERT: R 357 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8029 (ttp80) REVERT: R 403 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7423 (ptp-170) outliers start: 39 outliers final: 26 residues processed: 225 average time/residue: 0.3655 time to fit residues: 90.5145 Evaluate side-chains 233 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 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 403 ARG Chi-restraints excluded: chain R residue 458 LYS Chi-restraints excluded: chain R residue 481 ASN Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 170 HIS D 34 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108206 restraints weight = 14175.333| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.89 r_work: 0.3368 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10191 Z= 0.204 Angle : 0.639 9.474 13882 Z= 0.324 Chirality : 0.046 0.214 1543 Planarity : 0.006 0.146 1772 Dihedral : 5.222 42.764 1473 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 4.17 % Allowed : 13.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1280 helix: -1.99 (0.80), residues: 41 sheet: 0.76 (0.22), residues: 554 loop : -0.61 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.017 0.002 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.012 0.002 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 (10174) covalent geometry : angle 0.63261 / 0.32 (13845) SS BOND : bond 0.00795 / 0.47 ( 14) SS BOND : angle 1.86599 / 1.40 ( 28) hydrogen bonds : bond 0.03933 / 2.66 ( 357) hydrogen bonds : angle 5.59698 / 3.81 ( 978) link_BETA1-4 : bond 0.00254 / 0.13 ( 1) link_BETA1-4 : angle 1.71710 / 0.91 ( 3) link_BETA1-6 : bond 0.00098 / 0.05 ( 1) link_BETA1-6 : angle 1.41494 / 0.78 ( 3) link_NAG-ASN : bond 0.00343 / 0.18 ( 1) link_NAG-ASN : angle 2.27497 / 1.28 ( 3) *********************** 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 249 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.395 Fit side-chains REVERT: A 119 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 177 VAL cc_start: 0.8474 (t) cc_final: 0.8258 (p) REVERT: A 223 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7315 (tttt) REVERT: B 170 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6987 (p0) REVERT: D 90 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (pp30) REVERT: D 164 VAL cc_start: 0.8530 (t) cc_final: 0.8308 (p) REVERT: H 4 LEU cc_start: 0.8912 (mt) cc_final: 0.8586 (mt) REVERT: H 38 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7236 (ptp-170) REVERT: H 112 GLN cc_start: 0.7571 (mp10) cc_final: 0.7262 (mp10) REVERT: R 335 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8026 (mp) REVERT: R 357 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8032 (ttp80) REVERT: R 403 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7422 (ptp-170) outliers start: 46 outliers final: 31 residues processed: 226 average time/residue: 0.3672 time to fit residues: 91.4935 Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 A residue 212 VAL 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 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 159 ASN 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 30 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 9 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 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 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3865 r_free = 0.3865 target = 0.135081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109236 restraints weight = 14210.553| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.91 r_work: 0.3387 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10191 Z= 0.127 Angle : 0.591 11.658 13882 Z= 0.298 Chirality : 0.043 0.207 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.058 41.836 1473 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.33 % Rotamer: Outliers : 3.18 % Allowed : 15.15 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1280 helix: -1.90 (0.80), residues: 41 sheet: 0.80 (0.22), residues: 554 loop : -0.55 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 357 TYR 0.014 0.001 TYR C 33 PHE 0.021 0.001 PHE C 27 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10174) covalent geometry : angle 0.58682 / 0.30 (13845) SS BOND : bond 0.00571 / 0.34 ( 14) SS BOND : angle 1.44505 / 1.06 ( 28) hydrogen bonds : bond 0.03390 / 2.29 ( 357) hydrogen bonds : angle 5.39535 / 3.67 ( 978) link_BETA1-4 : bond 0.00323 / 0.17 ( 1) link_BETA1-4 : angle 1.50722 / 0.80 ( 3) link_BETA1-6 : bond 0.00181 / 0.10 ( 1) link_BETA1-6 : angle 1.30444 / 0.72 ( 3) link_NAG-ASN : bond 0.00382 / 0.20 ( 1) link_NAG-ASN : angle 1.90927 / 1.08 ( 3) *********************** 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 238 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.299 Fit side-chains REVERT: A 119 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 177 VAL cc_start: 0.8455 (t) cc_final: 0.8235 (p) REVERT: A 223 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7302 (tttt) REVERT: B 146 VAL cc_start: 0.7869 (m) cc_final: 0.7625 (t) REVERT: B 170 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6980 (p0) REVERT: D 90 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: D 164 VAL cc_start: 0.8527 (t) cc_final: 0.8306 (p) REVERT: H 4 LEU cc_start: 0.8905 (mt) cc_final: 0.8587 (mt) REVERT: H 112 GLN cc_start: 0.7525 (mp10) cc_final: 0.7229 (mp10) REVERT: R 335 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8008 (mp) REVERT: R 357 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8024 (ttp80) REVERT: R 403 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7421 (ptp-170) outliers start: 35 outliers final: 24 residues processed: 221 average time/residue: 0.3563 time to fit residues: 87.1875 Evaluate side-chains 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 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 371 PHE 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 83 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 88 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 170 HIS D 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108667 restraints weight = 14189.951| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.89 r_work: 0.3374 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10191 Z= 0.188 Angle : 0.623 10.725 13882 Z= 0.316 Chirality : 0.045 0.213 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.146 42.309 1473 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 4.26 % Allowed : 14.16 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1280 helix: -1.91 (0.80), residues: 41 sheet: 0.80 (0.22), residues: 554 loop : -0.59 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.016 0.002 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.012 0.002 TRP A 47 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (10174) covalent geometry : angle 0.61653 / 0.31 (13845) SS BOND : bond 0.00755 / 0.45 ( 14) SS BOND : angle 1.76580 / 1.32 ( 28) hydrogen bonds : bond 0.03737 / 2.52 ( 357) hydrogen bonds : angle 5.42695 / 3.69 ( 978) link_BETA1-4 : bond 0.00339 / 0.18 ( 1) link_BETA1-4 : angle 1.67103 / 0.89 ( 3) link_BETA1-6 : bond 0.00252 / 0.13 ( 1) link_BETA1-6 : angle 1.42031 / 0.78 ( 3) link_NAG-ASN : bond 0.00339 / 0.18 ( 1) link_NAG-ASN : angle 2.23444 / 1.25 ( 3) *********************** 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 248 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.241 Fit side-chains REVERT: A 119 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: A 177 VAL cc_start: 0.8484 (t) cc_final: 0.8275 (p) REVERT: A 223 LYS cc_start: 0.7586 (ttmm) cc_final: 0.7309 (tttt) REVERT: B 170 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6996 (p0) REVERT: D 90 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8440 (pp30) REVERT: D 164 VAL cc_start: 0.8534 (t) cc_final: 0.8325 (p) REVERT: H 4 LEU cc_start: 0.8918 (mt) cc_final: 0.8602 (mt) REVERT: H 38 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7255 (ptp-170) REVERT: H 112 GLN cc_start: 0.7545 (mp10) cc_final: 0.7262 (mp10) REVERT: R 335 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8015 (mp) REVERT: R 357 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8037 (ttp80) REVERT: R 403 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7414 (ptp-170) outliers start: 47 outliers final: 30 residues processed: 229 average time/residue: 0.3281 time to fit residues: 82.8249 Evaluate side-chains 238 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER 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 156 SER Chi-restraints excluded: chain B residue 170 ASP 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 D residue 159 ASN 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 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG 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 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 116 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.884 > 50:) chunk 91 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3866 r_free = 0.3866 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109462 restraints weight = 14111.585| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.90 r_work: 0.3385 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10191 Z= 0.141 Angle : 0.608 10.227 13882 Z= 0.306 Chirality : 0.044 0.208 1543 Planarity : 0.006 0.145 1772 Dihedral : 5.067 41.656 1473 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 3.72 % Allowed : 14.61 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1280 helix: -1.88 (0.80), residues: 41 sheet: 0.83 (0.22), residues: 554 loop : -0.55 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 357 TYR 0.014 0.001 TYR C 33 PHE 0.021 0.001 PHE C 27 TRP 0.012 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (10174) covalent geometry : angle 0.60123 / 0.30 (13845) SS BOND : bond 0.00612 / 0.36 ( 14) SS BOND : angle 1.87438 / 1.28 ( 28) hydrogen bonds : bond 0.03436 / 2.32 ( 357) hydrogen bonds : angle 5.32518 / 3.62 ( 978) link_BETA1-4 : bond 0.00301 / 0.16 ( 1) link_BETA1-4 : angle 1.55465 / 0.82 ( 3) link_BETA1-6 : bond 0.00132 / 0.07 ( 1) link_BETA1-6 : angle 1.33230 / 0.74 ( 3) link_NAG-ASN : bond 0.00374 / 0.20 ( 1) link_NAG-ASN : angle 2.01959 / 1.14 ( 3) *********************** 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 243 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.234 Fit side-chains REVERT: A 119 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 177 VAL cc_start: 0.8472 (t) cc_final: 0.8259 (p) REVERT: A 223 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7290 (tttt) REVERT: B 146 VAL cc_start: 0.7893 (m) cc_final: 0.7662 (t) REVERT: B 170 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6987 (p0) REVERT: B 178 THR cc_start: 0.8535 (m) cc_final: 0.8208 (t) REVERT: D 90 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: D 164 VAL cc_start: 0.8540 (t) cc_final: 0.8335 (p) REVERT: D 171 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7122 (p0) REVERT: H 4 LEU cc_start: 0.8907 (mt) cc_final: 0.8598 (mt) REVERT: H 38 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: H 112 GLN cc_start: 0.7515 (mp10) cc_final: 0.7227 (mp10) REVERT: R 357 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8036 (ttp80) REVERT: R 403 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7416 (ptp-170) outliers start: 41 outliers final: 30 residues processed: 224 average time/residue: 0.3185 time to fit residues: 78.5736 Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER 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 A residue 215 LYS 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 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 90 GLN 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 38 ARG Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN B 6 GLN C 76 ASN D 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.109524 restraints weight = 14102.328| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.90 r_work: 0.3375 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.004 0.059 10191 Z= 0.184 Angle : 0.628 10.566 13882 Z= 0.316 Chirality : 0.045 0.213 1543 Planarity : 0.006 0.146 1772 Dihedral : 5.128 41.931 1473 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.54 % Allowed : 15.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1280 helix: -1.86 (0.81), residues: 41 sheet: 0.82 (0.22), residues: 554 loop : -0.59 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.016 0.001 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (10174) covalent geometry : angle 0.62088 / 0.31 (13845) SS BOND : bond 0.00727 / 0.44 ( 14) SS BOND : angle 1.95659 / 1.37 ( 28) hydrogen bonds : bond 0.03649 / 2.47 ( 357) hydrogen bonds : angle 5.36917 / 3.65 ( 978) link_BETA1-4 : bond 0.00278 / 0.15 ( 1) link_BETA1-4 : angle 1.63145 / 0.87 ( 3) link_BETA1-6 : bond 0.00017 / 0.01 ( 1) link_BETA1-6 : angle 1.38240 / 0.76 ( 3) link_NAG-ASN : bond 0.00347 / 0.18 ( 1) link_NAG-ASN : angle 2.19454 / 1.23 ( 3) *********************** 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 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.349 Fit side-chains REVERT: A 119 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: A 177 VAL cc_start: 0.8489 (t) cc_final: 0.8284 (p) REVERT: A 223 LYS cc_start: 0.7589 (ttmm) cc_final: 0.7301 (tttt) REVERT: B 146 VAL cc_start: 0.7907 (m) cc_final: 0.7680 (t) REVERT: B 170 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6992 (p0) REVERT: B 178 THR cc_start: 0.8551 (m) cc_final: 0.8225 (t) REVERT: D 171 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7126 (p0) REVERT: H 4 LEU cc_start: 0.8919 (mt) cc_final: 0.8618 (mt) REVERT: H 38 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7258 (ptp-170) REVERT: H 112 GLN cc_start: 0.7503 (mp10) cc_final: 0.7221 (mp10) REVERT: R 357 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: R 403 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7414 (ptp-170) outliers start: 39 outliers final: 32 residues processed: 221 average time/residue: 0.3578 time to fit residues: 86.7229 Evaluate side-chains 234 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER 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 A residue 215 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 159 ASN 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 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 458 LYS Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN D 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108712 restraints weight = 14073.384| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.89 r_work: 0.3381 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 10191 Z= 0.221 Angle : 0.900 59.200 13882 Z= 0.513 Chirality : 0.047 0.538 1543 Planarity : 0.006 0.146 1772 Dihedral : 4.921 41.839 1470 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.63 % Allowed : 15.25 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1280 helix: -1.86 (0.81), residues: 41 sheet: 0.82 (0.22), residues: 554 loop : -0.60 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.016 0.001 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (10174) covalent geometry : angle 0.89518 / 0.51 (13845) SS BOND : bond 0.00809 / 0.55 ( 14) SS BOND : angle 2.10807 / 1.45 ( 28) hydrogen bonds : bond 0.03631 / 2.46 ( 357) hydrogen bonds : angle 5.36777 / 3.65 ( 978) link_BETA1-4 : bond 0.00193 / 0.10 ( 1) link_BETA1-4 : angle 1.65772 / 0.88 ( 3) link_BETA1-6 : bond 0.00149 / 0.08 ( 1) link_BETA1-6 : angle 1.47015 / 0.81 ( 3) link_NAG-ASN : bond 0.00357 / 0.19 ( 1) link_NAG-ASN : angle 2.19013 / 1.23 ( 3) ********************** 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 236 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.260 Fit side-chains REVERT: A 119 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: A 177 VAL cc_start: 0.8490 (t) cc_final: 0.8282 (p) REVERT: A 223 LYS cc_start: 0.7589 (ttmm) cc_final: 0.7299 (tttt) REVERT: B 146 VAL cc_start: 0.7905 (m) cc_final: 0.7676 (t) REVERT: B 170 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6990 (p0) REVERT: B 178 THR cc_start: 0.8552 (m) cc_final: 0.8226 (t) REVERT: D 90 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8443 (pp30) REVERT: D 171 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7120 (p0) REVERT: H 4 LEU cc_start: 0.8917 (mt) cc_final: 0.8617 (mt) REVERT: H 38 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7254 (ptp-170) REVERT: H 112 GLN cc_start: 0.7500 (mp10) cc_final: 0.7216 (mp10) REVERT: R 357 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8049 (ttp80) REVERT: R 403 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7411 (ptp-170) outliers start: 40 outliers final: 31 residues processed: 219 average time/residue: 0.3443 time to fit residues: 82.9087 Evaluate side-chains 234 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER 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 A residue 215 LYS 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 170 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 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 38 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 458 LYS Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 92 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3856 r_free = 0.3856 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108646 restraints weight = 14281.162| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.90 r_work: 0.3379 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 10191 Z= 0.223 Angle : 0.901 59.200 13882 Z= 0.513 Chirality : 0.047 0.538 1543 Planarity : 0.006 0.146 1772 Dihedral : 4.921 41.839 1470 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 3.45 % Allowed : 15.43 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1280 helix: -1.86 (0.81), residues: 41 sheet: 0.82 (0.22), residues: 554 loop : -0.60 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.016 0.001 TYR C 33 PHE 0.021 0.002 PHE C 27 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (10174) covalent geometry : angle 0.89518 / 0.51 (13845) SS BOND : bond 0.01927 / 1.62 ( 14) SS BOND : angle 2.26653 / 1.51 ( 28) hydrogen bonds : bond 0.03631 / 2.46 ( 357) hydrogen bonds : angle 5.36777 / 3.65 ( 978) link_BETA1-4 : bond 0.00193 / 0.10 ( 1) link_BETA1-4 : angle 1.65772 / 0.88 ( 3) link_BETA1-6 : bond 0.00149 / 0.08 ( 1) link_BETA1-6 : angle 1.47015 / 0.81 ( 3) link_NAG-ASN : bond 0.00357 / 0.19 ( 1) link_NAG-ASN : angle 2.19013 / 1.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.04 seconds wall clock time: 66 minutes 19.47 seconds (3979.47 seconds total)