Starting phenix.real_space_refine on Wed Apr 30 21:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpw_37725/04_2025/8wpw_37725_neut.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6274 2.51 5 N 1654 2.21 5 O 1964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9930 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "B" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1659 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 13, 'TRANS': 207} Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1619 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "R" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 14, 'TRANS': 180} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.18, per 1000 atoms: 0.62 Number of scatterers: 9930 At special positions: 0 Unit cell: (86.7, 105.4, 171.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1964 8.00 N 1654 7.00 C 6274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG E 1 " - " ASN R 343 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 10.5% alpha, 45.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.022A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.009A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.975A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.701A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.774A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.950A pdb=" N THR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.886A pdb=" N GLN D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS D 127 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 removed outlier: 3.734A pdb=" N GLU D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 184 through 188' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.757A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.217A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 371 Processing helix chain 'R' and resid 383 through 387 Processing helix chain 'R' and resid 405 through 410 removed outlier: 5.079A pdb=" N SER R 408 " --> pdb=" O ASN R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.759A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.100A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 removed outlier: 3.749A pdb=" N GLY A 153 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 removed outlier: 3.749A pdb=" N GLY A 153 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 removed outlier: 3.844A pdb=" N THR A 165 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 208 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS A 214 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.670A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.914A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 138 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 133 Processing sheet with id=AB3, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.867A pdb=" N LYS B 207 " --> pdb=" O CYS B 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.722A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.152A pdb=" N TYR C 33 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS C 95 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP C 109 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG C 97 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 126 through 129 removed outlier: 6.187A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 126 through 129 removed outlier: 6.187A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.586A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.369A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.369A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.722A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 133 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.118A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.757A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 104 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.110A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.837A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.837A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 93 through 94 Processing sheet with id=AD4, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'R' and resid 473 through 474 408 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.69 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: 3.210 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.990 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 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 : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 1.63 % Allowed : 4.08 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1280 helix: -2.51 (0.72), residues: 39 sheet: 0.73 (0.23), residues: 534 loop : -0.38 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 109 HIS 0.003 0.001 HIS B 92 PHE 0.011 0.001 PHE C 27 TYR 0.012 0.001 TYR C 33 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 1) link_NAG-ASN : angle 1.89634 ( 3) link_BETA1-4 : bond 0.00195 ( 1) link_BETA1-4 : angle 1.66434 ( 3) hydrogen bonds : bond 0.24702 ( 357) hydrogen bonds : angle 9.28094 ( 978) link_BETA1-6 : bond 0.00173 ( 1) link_BETA1-6 : angle 1.72208 ( 3) SS BOND : bond 0.00430 ( 14) SS BOND : angle 0.75558 ( 28) covalent geometry : bond 0.00277 (10174) covalent geometry : angle 0.50323 (13845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2560 Ramachandran restraints generated. 1280 Oldfield, 0 Emsley, 1280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.141 Fit side-chains REVERT: A 194 SER cc_start: 0.8549 (t) cc_final: 0.8267 (m) REVERT: A 212 VAL cc_start: 0.7923 (t) cc_final: 0.7697 (m) REVERT: B 83 ASP cc_start: 0.7559 (m-30) cc_final: 0.6956 (m-30) REVERT: B 105 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6707 (mt-10) REVERT: B 141 PRO cc_start: 0.6244 (Cg_exo) cc_final: 0.6014 (Cg_endo) REVERT: C 31 TYR cc_start: 0.8478 (m-10) cc_final: 0.8241 (m-10) REVERT: D 90 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (pp30) REVERT: D 163 SER cc_start: 0.8047 (t) cc_final: 0.7847 (p) REVERT: D 164 VAL cc_start: 0.8240 (t) cc_final: 0.7989 (p) REVERT: H 112 GLN cc_start: 0.6895 (mp10) cc_final: 0.6618 (mp10) REVERT: L 108 LYS cc_start: 0.8042 (pttm) cc_final: 0.7467 (mmtt) REVERT: R 420 ASP cc_start: 0.7811 (m-30) cc_final: 0.7587 (m-30) REVERT: R 460 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8526 (mtmt) outliers start: 18 outliers final: 5 residues processed: 271 average time/residue: 0.7269 time to fit residues: 219.5773 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 : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS C 39 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110357 restraints weight = 13978.208| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.87 r_work: 0.3401 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10191 Z= 0.130 Angle : 0.587 8.978 13882 Z= 0.302 Chirality : 0.044 0.213 1543 Planarity : 0.006 0.145 1772 Dihedral : 4.984 41.142 1476 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.33 % Rotamer: Outliers : 3.27 % Allowed : 10.89 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1280 helix: -2.16 (0.76), residues: 41 sheet: 0.81 (0.23), residues: 557 loop : -0.42 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 189 PHE 0.023 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 1) link_NAG-ASN : angle 1.26607 ( 3) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.46024 ( 3) hydrogen bonds : bond 0.04381 ( 357) hydrogen bonds : angle 6.29511 ( 978) link_BETA1-6 : bond 0.00310 ( 1) link_BETA1-6 : angle 1.73909 ( 3) SS BOND : bond 0.00604 ( 14) SS BOND : angle 1.49822 ( 28) covalent geometry : bond 0.00295 (10174) covalent geometry : angle 0.58277 (13845) *********************** 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 236 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.996 Fit side-chains REVERT: A 119 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: A 223 LYS cc_start: 0.7540 (ttmm) cc_final: 0.7298 (tttt) REVERT: B 82 GLU cc_start: 0.7139 (pm20) cc_final: 0.6858 (pm20) REVERT: B 141 PRO cc_start: 0.6634 (Cg_exo) cc_final: 0.6421 (Cg_endo) REVERT: B 197 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7816 (p) REVERT: D 90 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8410 (pp30) REVERT: H 4 LEU cc_start: 0.8845 (mt) cc_final: 0.8489 (mt) REVERT: H 112 GLN cc_start: 0.7655 (mp10) cc_final: 0.7331 (mp10) REVERT: R 335 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (mp) REVERT: R 403 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7545 (ptp-170) REVERT: R 420 ASP cc_start: 0.8113 (m-30) cc_final: 0.7901 (m-30) REVERT: R 460 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8624 (mtmt) outliers start: 36 outliers final: 14 residues processed: 220 average time/residue: 0.9125 time to fit residues: 221.7897 Evaluate side-chains 206 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 0.0020 chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 77 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 GLN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.111309 restraints weight = 14282.017| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.92 r_work: 0.3410 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 10191 Z= 0.101 Angle : 0.557 10.574 13882 Z= 0.282 Chirality : 0.043 0.212 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.811 40.406 1473 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 13.34 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1280 helix: -1.90 (0.80), residues: 41 sheet: 0.83 (0.23), residues: 556 loop : -0.34 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS C 206 PHE 0.020 0.001 PHE C 27 TYR 0.012 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 1) link_NAG-ASN : angle 1.34130 ( 3) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 1.44890 ( 3) hydrogen bonds : bond 0.03492 ( 357) hydrogen bonds : angle 5.66454 ( 978) link_BETA1-6 : bond 0.00074 ( 1) link_BETA1-6 : angle 1.33247 ( 3) SS BOND : bond 0.00440 ( 14) SS BOND : angle 1.25708 ( 28) covalent geometry : bond 0.00234 (10174) covalent geometry : angle 0.55332 (13845) *********************** 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 224 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.196 Fit side-chains REVERT: A 119 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: A 223 LYS cc_start: 0.7520 (ttmm) cc_final: 0.7315 (tttt) REVERT: B 141 PRO cc_start: 0.6623 (Cg_exo) cc_final: 0.6417 (Cg_endo) REVERT: D 90 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: D 164 VAL cc_start: 0.8542 (t) cc_final: 0.8316 (p) REVERT: R 403 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7533 (ptp-170) REVERT: R 460 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8670 (mtmt) outliers start: 28 outliers final: 14 residues processed: 211 average time/residue: 1.0376 time to fit residues: 241.3054 Evaluate side-chains 205 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU 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 62 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 403 ARG 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 14 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 76 ASN C 170 HIS D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109694 restraints weight = 14026.924| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.90 r_work: 0.3393 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10191 Z= 0.151 Angle : 0.585 8.904 13882 Z= 0.297 Chirality : 0.044 0.218 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.923 41.060 1473 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 3.27 % Allowed : 13.79 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1280 helix: -1.77 (0.83), residues: 41 sheet: 0.79 (0.22), residues: 557 loop : -0.41 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.016 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 1.85728 ( 3) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.57325 ( 3) hydrogen bonds : bond 0.03621 ( 357) hydrogen bonds : angle 5.48957 ( 978) link_BETA1-6 : bond 0.00106 ( 1) link_BETA1-6 : angle 1.34282 ( 3) SS BOND : bond 0.00658 ( 14) SS BOND : angle 1.45535 ( 28) covalent geometry : bond 0.00366 (10174) covalent geometry : angle 0.58109 (13845) *********************** 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 235 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.119 Fit side-chains REVERT: A 119 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: A 223 LYS cc_start: 0.7548 (ttmm) cc_final: 0.7315 (tttt) REVERT: B 146 VAL cc_start: 0.7849 (m) cc_final: 0.7602 (t) REVERT: D 90 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8444 (pp30) REVERT: D 164 VAL cc_start: 0.8526 (t) cc_final: 0.8277 (p) REVERT: R 335 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7975 (mp) REVERT: R 357 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8050 (ttp80) REVERT: R 403 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7526 (ptp-170) outliers start: 36 outliers final: 22 residues processed: 220 average time/residue: 0.8497 time to fit residues: 205.9665 Evaluate side-chains 222 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.0040 chunk 16 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 76 ASN C 170 HIS ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.136864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111024 restraints weight = 14145.144| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.90 r_work: 0.3404 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10191 Z= 0.116 Angle : 0.572 11.359 13882 Z= 0.286 Chirality : 0.043 0.212 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.833 40.571 1473 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 13.70 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1280 helix: -1.76 (0.81), residues: 41 sheet: 0.84 (0.22), residues: 554 loop : -0.40 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 1) link_NAG-ASN : angle 1.66337 ( 3) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.40086 ( 3) hydrogen bonds : bond 0.03194 ( 357) hydrogen bonds : angle 5.21373 ( 978) link_BETA1-6 : bond 0.00249 ( 1) link_BETA1-6 : angle 1.32040 ( 3) SS BOND : bond 0.00504 ( 14) SS BOND : angle 1.42859 ( 28) covalent geometry : bond 0.00280 (10174) covalent geometry : angle 0.56832 (13845) *********************** 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 233 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.962 Fit side-chains REVERT: A 119 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 223 LYS cc_start: 0.7559 (ttmm) cc_final: 0.7293 (tttt) REVERT: B 146 VAL cc_start: 0.7839 (m) cc_final: 0.7609 (t) REVERT: D 90 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (pp30) REVERT: D 164 VAL cc_start: 0.8524 (t) cc_final: 0.8294 (p) REVERT: R 335 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7963 (mp) REVERT: R 357 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8022 (ttp80) REVERT: R 403 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7518 (ptp-170) outliers start: 38 outliers final: 27 residues processed: 217 average time/residue: 0.8686 time to fit residues: 207.8119 Evaluate side-chains 224 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 165 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 77 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 76 ASN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110949 restraints weight = 14144.839| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.90 r_work: 0.3403 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10191 Z= 0.121 Angle : 0.569 9.852 13882 Z= 0.286 Chirality : 0.043 0.214 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.811 40.596 1473 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 3.90 % Allowed : 14.07 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1280 helix: -1.70 (0.82), residues: 41 sheet: 0.88 (0.22), residues: 554 loop : -0.44 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 1.83051 ( 3) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 1.48078 ( 3) hydrogen bonds : bond 0.03158 ( 357) hydrogen bonds : angle 5.14155 ( 978) link_BETA1-6 : bond 0.00213 ( 1) link_BETA1-6 : angle 1.28944 ( 3) SS BOND : bond 0.00538 ( 14) SS BOND : angle 1.40980 ( 28) covalent geometry : bond 0.00293 (10174) covalent geometry : angle 0.56534 (13845) *********************** 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 235 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.987 Fit side-chains REVERT: A 119 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 223 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7270 (tttt) REVERT: B 146 VAL cc_start: 0.7862 (m) cc_final: 0.7641 (t) REVERT: D 164 VAL cc_start: 0.8551 (t) cc_final: 0.8330 (p) REVERT: R 357 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8010 (ttp80) REVERT: R 386 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: R 403 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7462 (ptp-170) outliers start: 43 outliers final: 31 residues processed: 214 average time/residue: 0.8594 time to fit residues: 201.8999 Evaluate side-chains 227 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 123 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111025 restraints weight = 14269.323| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.91 r_work: 0.3403 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10191 Z= 0.120 Angle : 0.569 9.049 13882 Z= 0.288 Chirality : 0.043 0.214 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.554 40.286 1470 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 3.54 % Allowed : 14.43 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1280 helix: -1.70 (0.82), residues: 41 sheet: 0.86 (0.22), residues: 558 loop : -0.43 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.014 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 1) link_NAG-ASN : angle 1.78436 ( 3) link_BETA1-4 : bond 0.00220 ( 1) link_BETA1-4 : angle 1.44533 ( 3) hydrogen bonds : bond 0.03136 ( 357) hydrogen bonds : angle 5.10449 ( 978) link_BETA1-6 : bond 0.00064 ( 1) link_BETA1-6 : angle 1.23489 ( 3) SS BOND : bond 0.00528 ( 14) SS BOND : angle 1.66033 ( 28) covalent geometry : bond 0.00291 (10174) covalent geometry : angle 0.56379 (13845) *********************** 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 230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.022 Fit side-chains REVERT: A 119 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 223 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7256 (tttt) REVERT: B 146 VAL cc_start: 0.7798 (m) cc_final: 0.7590 (t) REVERT: D 90 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: D 164 VAL cc_start: 0.8551 (t) cc_final: 0.8335 (p) REVERT: R 357 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8013 (ttp80) REVERT: R 386 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8289 (mptt) REVERT: R 403 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7462 (ptp-170) outliers start: 39 outliers final: 34 residues processed: 212 average time/residue: 0.9780 time to fit residues: 231.0634 Evaluate side-chains 230 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109569 restraints weight = 14195.824| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.90 r_work: 0.3390 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10191 Z= 0.160 Angle : 0.600 8.777 13882 Z= 0.305 Chirality : 0.044 0.217 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.687 40.887 1470 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 14.79 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1280 helix: -1.77 (0.81), residues: 41 sheet: 0.86 (0.22), residues: 554 loop : -0.49 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.002 PHE C 27 TYR 0.016 0.001 TYR C 33 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 1) link_NAG-ASN : angle 2.13800 ( 3) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 1.62688 ( 3) hydrogen bonds : bond 0.03433 ( 357) hydrogen bonds : angle 5.20620 ( 978) link_BETA1-6 : bond 0.00221 ( 1) link_BETA1-6 : angle 1.35673 ( 3) SS BOND : bond 0.00684 ( 14) SS BOND : angle 1.83672 ( 28) covalent geometry : bond 0.00390 (10174) covalent geometry : angle 0.59366 (13845) *********************** 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 236 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.133 Fit side-chains REVERT: A 119 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 177 VAL cc_start: 0.8420 (t) cc_final: 0.8189 (p) REVERT: A 223 LYS cc_start: 0.7536 (ttmm) cc_final: 0.7235 (tttt) REVERT: B 146 VAL cc_start: 0.7888 (m) cc_final: 0.7678 (t) REVERT: D 90 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8446 (pp30) REVERT: R 357 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8064 (ttp80) REVERT: R 386 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8319 (mptt) REVERT: R 403 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7414 (ptp-170) outliers start: 44 outliers final: 34 residues processed: 215 average time/residue: 0.9049 time to fit residues: 213.3739 Evaluate side-chains 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 165 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 chunk 27 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110378 restraints weight = 14207.560| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.90 r_work: 0.3401 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1907 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= 0.117 Angle : 0.573 8.761 13882 Z= 0.290 Chirality : 0.043 0.211 1543 Planarity : 0.005 0.144 1772 Dihedral : 4.617 40.303 1470 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1280 helix: -1.78 (0.80), residues: 41 sheet: 0.88 (0.22), residues: 554 loop : -0.47 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.003 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.013 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 1.86582 ( 3) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.48669 ( 3) hydrogen bonds : bond 0.03131 ( 357) hydrogen bonds : angle 5.11023 ( 978) link_BETA1-6 : bond 0.00255 ( 1) link_BETA1-6 : angle 1.29411 ( 3) SS BOND : bond 0.00524 ( 14) SS BOND : angle 1.54274 ( 28) covalent geometry : bond 0.00282 (10174) covalent geometry : angle 0.56856 (13845) *********************** 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 232 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.122 Fit side-chains REVERT: A 119 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 177 VAL cc_start: 0.8383 (t) cc_final: 0.8155 (p) REVERT: A 223 LYS cc_start: 0.7504 (ttmm) cc_final: 0.7232 (tttt) REVERT: B 146 VAL cc_start: 0.7798 (m) cc_final: 0.7596 (t) REVERT: D 90 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (pp30) REVERT: R 357 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: R 386 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8303 (mptt) REVERT: R 403 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7458 (ptp-170) outliers start: 39 outliers final: 33 residues processed: 212 average time/residue: 0.9754 time to fit residues: 227.8963 Evaluate side-chains 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 165 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG 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 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109383 restraints weight = 14201.714| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.89 r_work: 0.3384 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: 0.8166 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10191 Z= 0.169 Angle : 0.615 8.801 13882 Z= 0.312 Chirality : 0.045 0.217 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.757 41.085 1470 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Rotamer: Outliers : 3.45 % Allowed : 15.61 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1280 helix: -1.83 (0.80), residues: 41 sheet: 0.87 (0.22), residues: 554 loop : -0.53 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 109 HIS 0.004 0.001 HIS B 92 PHE 0.020 0.002 PHE C 27 TYR 0.016 0.001 TYR C 33 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 1) link_NAG-ASN : angle 2.10807 ( 3) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 1.61867 ( 3) hydrogen bonds : bond 0.03506 ( 357) hydrogen bonds : angle 5.22187 ( 978) link_BETA1-6 : bond 0.00187 ( 1) link_BETA1-6 : angle 1.37585 ( 3) SS BOND : bond 0.00721 ( 14) SS BOND : angle 1.90889 ( 28) covalent geometry : bond 0.00411 (10174) covalent geometry : angle 0.60773 (13845) ********************** 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 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.799 Fit side-chains REVERT: A 119 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 177 VAL cc_start: 0.8439 (t) cc_final: 0.8215 (p) REVERT: B 146 VAL cc_start: 0.7896 (m) cc_final: 0.7693 (t) REVERT: B 171 SER cc_start: 0.8221 (m) cc_final: 0.8005 (p) REVERT: D 90 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8444 (pp30) REVERT: R 357 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: R 386 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: R 403 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7424 (ptp-170) outliers start: 38 outliers final: 30 residues processed: 210 average time/residue: 1.0423 time to fit residues: 240.6095 Evaluate side-chains 226 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 197 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 356 LYS Chi-restraints excluded: chain R residue 357 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 371 PHE Chi-restraints excluded: chain R residue 386 LYS Chi-restraints excluded: chain R residue 403 ARG Chi-restraints excluded: chain R residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN D 34 ASN ** D 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109686 restraints weight = 14128.603| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.88 r_work: 0.3387 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10191 Z= 0.157 Angle : 0.607 8.830 13882 Z= 0.307 Chirality : 0.044 0.212 1543 Planarity : 0.005 0.145 1772 Dihedral : 4.750 40.752 1470 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 3.18 % Allowed : 15.88 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1280 helix: -1.87 (0.79), residues: 41 sheet: 0.86 (0.22), residues: 554 loop : -0.53 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS B 92 PHE 0.020 0.001 PHE C 27 TYR 0.015 0.001 TYR C 33 ARG 0.003 0.000 ARG R 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 1) link_NAG-ASN : angle 2.05813 ( 3) link_BETA1-4 : bond 0.00274 ( 1) link_BETA1-4 : angle 1.55480 ( 3) hydrogen bonds : bond 0.03369 ( 357) hydrogen bonds : angle 5.18873 ( 978) link_BETA1-6 : bond 0.00085 ( 1) link_BETA1-6 : angle 1.32578 ( 3) SS BOND : bond 0.00642 ( 14) SS BOND : angle 1.81301 ( 28) covalent geometry : bond 0.00383 (10174) covalent geometry : angle 0.60103 (13845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10193.46 seconds wall clock time: 177 minutes 20.73 seconds (10640.73 seconds total)