Starting phenix.real_space_refine on Thu Jul 2 05:17:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.map" model { file = "/net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r41_53561/07_2026/9r41_53561.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 49 5.16 5 C 4307 2.51 5 N 1142 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6742 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2476 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 320 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2094 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'CLR': 1, 'T7M': 1, 'YLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'T7M:plan-2': 1, 'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.67, per 1000 atoms: 0.25 Number of scatterers: 6742 At special positions: 0 Unit cell: (93.28, 106, 103.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 2 15.00 O 1242 8.00 N 1142 7.00 C 4307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 394.7 milliseconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 48.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.792A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.649A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.519A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.826A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.661A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.819A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.025A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 4.002A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.501A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.844A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 removed outlier: 3.933A pdb=" N LEU R 74 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 174 removed outlier: 3.871A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 226 Processing helix chain 'R' and resid 328 through 368 removed outlier: 4.207A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 369 through 371 No H-bonds generated for 'chain 'R' and resid 369 through 371' Processing helix chain 'R' and resid 378 through 391 Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 414 removed outlier: 3.649A pdb=" N GLN R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.722A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.998A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.979A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.172A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.542A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.596A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.032A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.890A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1171 1.32 - 1.45: 1774 1.45 - 1.57: 3860 1.57 - 1.69: 3 1.69 - 1.82: 68 Bond restraints: 6876 Sorted by residual: bond pdb=" C4 YLX R 501 " pdb=" C5 YLX R 501 " ideal model delta sigma weight residual 1.546 1.453 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O4 T7M R 503 " pdb=" P4 T7M R 503 " ideal model delta sigma weight residual 1.704 1.626 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" N YLX R 501 " pdb=" C8 YLX R 501 " ideal model delta sigma weight residual 1.389 1.316 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O13 T7M R 503 " pdb=" P1 T7M R 503 " ideal model delta sigma weight residual 1.659 1.595 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N YLX R 501 " pdb=" C YLX R 501 " ideal model delta sigma weight residual 1.390 1.343 0.047 2.00e-02 2.50e+03 5.41e+00 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 9147 1.86 - 3.71: 153 3.71 - 5.57: 23 5.57 - 7.43: 7 7.43 - 9.29: 2 Bond angle restraints: 9332 Sorted by residual: angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 122.78 -8.38 2.30e+00 1.89e-01 1.33e+01 angle pdb=" N VAL R 98 " pdb=" CA VAL R 98 " pdb=" C VAL R 98 " ideal model delta sigma weight residual 110.53 113.58 -3.05 9.40e-01 1.13e+00 1.05e+01 angle pdb=" C1 YLX R 501 " pdb=" C2 YLX R 501 " pdb=" C7 YLX R 501 " ideal model delta sigma weight residual 106.31 115.60 -9.29 3.00e+00 1.11e-01 9.58e+00 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 114.22 -3.52 1.22e+00 6.72e-01 8.31e+00 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 120.79 -6.39 2.30e+00 1.89e-01 7.73e+00 ... (remaining 9327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 3954 27.89 - 55.77: 197 55.77 - 83.66: 19 83.66 - 111.55: 11 111.55 - 139.43: 8 Dihedral angle restraints: 4189 sinusoidal: 1685 harmonic: 2504 Sorted by residual: dihedral pdb=" C10 T7M R 503 " pdb=" C8 T7M R 503 " pdb=" O16 T7M R 503 " pdb=" C7 T7M R 503 " ideal model delta sinusoidal sigma weight residual 55.77 -83.66 139.43 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C10 T7M R 503 " pdb=" C8 T7M R 503 " pdb=" O16 T7M R 503 " pdb=" C9 T7M R 503 " ideal model delta sinusoidal sigma weight residual 288.02 155.61 132.41 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 127.56 -34.56 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 4186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 980 0.069 - 0.139: 102 0.139 - 0.208: 2 0.208 - 0.277: 0 0.277 - 0.346: 1 Chirality restraints: 1085 Sorted by residual: chirality pdb=" C8 T7M R 503 " pdb=" C7 T7M R 503 " pdb=" C9 T7M R 503 " pdb=" O16 T7M R 503 " both_signs ideal model delta sigma weight residual False -2.26 -2.61 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 T7M R 503 " pdb=" C1 T7M R 503 " pdb=" C3 T7M R 503 " pdb=" O2 T7M R 503 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1082 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N YLX R 501 " -0.049 2.00e-02 2.50e+03 4.38e-01 2.88e+03 pdb=" C YLX R 501 " -0.021 2.00e-02 2.50e+03 pdb=" O YLX R 501 " -0.522 2.00e-02 2.50e+03 pdb=" C1 YLX R 501 " 0.543 2.00e-02 2.50e+03 pdb=" C8 YLX R 501 " -0.514 2.00e-02 2.50e+03 pdb=" C9 YLX R 501 " 0.563 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 YLX R 501 " -0.025 2.00e-02 2.50e+03 1.86e-02 6.07e+00 pdb=" C16 YLX R 501 " 0.005 2.00e-02 2.50e+03 pdb=" C17 YLX R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C18 YLX R 501 " 0.004 2.00e-02 2.50e+03 pdb=" N2 YLX R 501 " 0.031 2.00e-02 2.50e+03 pdb=" N3 YLX R 501 " -0.016 2.00e-02 2.50e+03 pdb=" N4 YLX R 501 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 117 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C VAL R 117 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL R 117 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU R 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 476 2.73 - 3.28: 6790 3.28 - 3.82: 11386 3.82 - 4.36: 12865 4.36 - 4.90: 22901 Nonbonded interactions: 54418 Sorted by model distance: nonbonded pdb=" NH2 ARG G 27 " pdb=" O ILE G 28 " model vdw 2.193 3.120 nonbonded pdb=" O SER B 31 " pdb=" OG1 THR B 34 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.243 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.249 3.120 ... (remaining 54413 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 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 : 0.004 0.093 6878 Z= 0.202 Angle : 0.648 9.287 9336 Z= 0.349 Chirality : 0.043 0.346 1085 Planarity : 0.013 0.438 1160 Dihedral : 18.130 139.434 2559 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 845 helix: 2.34 (0.28), residues: 366 sheet: -0.15 (0.40), residues: 163 loop : -1.03 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.009 0.001 TYR R 96 PHE 0.011 0.001 PHE B 278 TRP 0.013 0.002 TRP B 297 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 ( 6876) covalent geometry : angle 0.64820 / 0.35 ( 9332) SS BOND : bond 0.01049 / 0.55 ( 2) SS BOND : angle 0.69692 / 0.33 ( 4) hydrogen bonds : bond 0.11623 / 8.26 ( 375) hydrogen bonds : angle 5.73074 / 4.01 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ILE cc_start: 0.5777 (mt) cc_final: 0.5103 (mt) REVERT: A 230 TYR cc_start: 0.6401 (p90) cc_final: 0.5730 (p90) REVERT: A 282 PRO cc_start: 0.3916 (Cg_endo) cc_final: 0.3376 (Cg_exo) REVERT: A 330 LYS cc_start: 0.5390 (mmtp) cc_final: 0.3676 (ttpp) REVERT: B 111 TYR cc_start: 0.7312 (m-80) cc_final: 0.7012 (m-80) REVERT: B 251 ARG cc_start: 0.6547 (mtt-85) cc_final: 0.6230 (mtt180) REVERT: R 143 ASP cc_start: 0.6384 (t70) cc_final: 0.5695 (t70) REVERT: R 349 ILE cc_start: 0.6696 (mt) cc_final: 0.6402 (mm) REVERT: R 412 LYS cc_start: 0.4909 (mttt) cc_final: 0.4625 (mttm) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0941 time to fit residues: 27.1237 Evaluate side-chains 147 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 213 HIS A 255 ASN A 269 ASN A 306 GLN R 126 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.201046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.172260 restraints weight = 7977.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176771 restraints weight = 4670.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179706 restraints weight = 3258.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.181822 restraints weight = 2549.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.183027 restraints weight = 2147.091| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6878 Z= 0.187 Angle : 0.751 11.194 9336 Z= 0.369 Chirality : 0.045 0.166 1085 Planarity : 0.004 0.041 1160 Dihedral : 10.514 108.175 1081 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.68 % Allowed : 15.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 845 helix: 2.16 (0.27), residues: 360 sheet: -0.45 (0.38), residues: 168 loop : -0.81 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 27 TYR 0.022 0.002 TYR A 287 PHE 0.019 0.002 PHE B 292 TRP 0.035 0.003 TRP R 125 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 6876) covalent geometry : angle 0.75072 / 0.37 ( 9332) SS BOND : bond 0.01139 / 0.60 ( 2) SS BOND : angle 0.92525 / 0.42 ( 4) hydrogen bonds : bond 0.03857 / 2.64 ( 375) hydrogen bonds : angle 4.98989 / 3.51 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.5520 (t0) cc_final: 0.5313 (t0) REVERT: A 230 TYR cc_start: 0.7038 (p90) cc_final: 0.6740 (p90) REVERT: A 251 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7643 (t70) REVERT: A 273 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6146 (tt) REVERT: A 331 ASN cc_start: 0.6102 (m-40) cc_final: 0.5729 (m-40) REVERT: B 111 TYR cc_start: 0.7365 (m-80) cc_final: 0.6614 (m-80) REVERT: R 87 VAL cc_start: 0.7817 (m) cc_final: 0.7408 (t) REVERT: R 92 MET cc_start: 0.7928 (mmm) cc_final: 0.7524 (mmt) REVERT: R 143 ASP cc_start: 0.7313 (t70) cc_final: 0.6297 (t0) REVERT: R 189 ILE cc_start: 0.4914 (OUTLIER) cc_final: 0.4614 (pt) REVERT: R 385 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7162 (tp) outliers start: 33 outliers final: 16 residues processed: 186 average time/residue: 0.0727 time to fit residues: 18.2544 Evaluate side-chains 156 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 385 ILE Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 0.0070 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN R 72 ASN R 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.199813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.172734 restraints weight = 7825.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.176766 restraints weight = 4800.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.179194 restraints weight = 3435.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.181277 restraints weight = 2750.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.182384 restraints weight = 2324.148| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6878 Z= 0.153 Angle : 0.649 8.346 9336 Z= 0.328 Chirality : 0.043 0.170 1085 Planarity : 0.004 0.040 1160 Dihedral : 8.527 105.227 1081 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.67 % Allowed : 17.16 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 845 helix: 2.07 (0.27), residues: 368 sheet: -0.25 (0.39), residues: 169 loop : -0.89 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 27 TYR 0.013 0.002 TYR R 195 PHE 0.010 0.002 PHE G 61 TRP 0.040 0.002 TRP R 125 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6876) covalent geometry : angle 0.64892 / 0.33 ( 9332) SS BOND : bond 0.00858 / 0.45 ( 2) SS BOND : angle 0.53581 / 0.25 ( 4) hydrogen bonds : bond 0.03705 / 2.56 ( 375) hydrogen bonds : angle 4.75272 / 3.34 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7751 (m-30) cc_final: 0.7434 (m-30) REVERT: A 33 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6214 (tt0) REVERT: A 315 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5998 (p0) REVERT: A 345 LYS cc_start: 0.7232 (mttt) cc_final: 0.6570 (mtmm) REVERT: B 234 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.5912 (t80) REVERT: B 333 ASP cc_start: 0.7426 (p0) cc_final: 0.7138 (p0) REVERT: R 87 VAL cc_start: 0.7728 (m) cc_final: 0.7477 (t) REVERT: R 92 MET cc_start: 0.7912 (mmm) cc_final: 0.7549 (mmt) REVERT: R 143 ASP cc_start: 0.7795 (t70) cc_final: 0.6787 (t70) REVERT: R 330 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5172 (tm-30) REVERT: R 356 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.5572 (mt) REVERT: R 385 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7152 (tp) outliers start: 40 outliers final: 23 residues processed: 183 average time/residue: 0.0616 time to fit residues: 15.5056 Evaluate side-chains 173 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 331 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.202528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175120 restraints weight = 7959.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.179390 restraints weight = 4773.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.182351 restraints weight = 3353.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.184189 restraints weight = 2617.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.185632 restraints weight = 2214.485| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6878 Z= 0.121 Angle : 0.611 8.403 9336 Z= 0.311 Chirality : 0.041 0.169 1085 Planarity : 0.003 0.041 1160 Dihedral : 8.344 101.147 1081 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.82 % Allowed : 19.01 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 845 helix: 2.08 (0.27), residues: 375 sheet: -0.35 (0.40), residues: 167 loop : -0.80 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 313 TYR 0.018 0.002 TYR A 287 PHE 0.010 0.001 PHE B 253 TRP 0.046 0.002 TRP R 125 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6876) covalent geometry : angle 0.61095 / 0.31 ( 9332) SS BOND : bond 0.00590 / 0.31 ( 2) SS BOND : angle 0.45613 / 0.21 ( 4) hydrogen bonds : bond 0.03415 / 2.34 ( 375) hydrogen bonds : angle 4.61858 / 3.25 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.176 Fit side-chains REVERT: A 33 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6185 (tt0) REVERT: A 253 ILE cc_start: 0.8525 (tp) cc_final: 0.8248 (tt) REVERT: A 315 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.6082 (p0) REVERT: A 345 LYS cc_start: 0.7171 (mttt) cc_final: 0.6527 (mtmm) REVERT: B 46 ARG cc_start: 0.5821 (mtm110) cc_final: 0.5075 (mmt180) REVERT: B 188 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7293 (mtt) REVERT: B 234 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6008 (t80) REVERT: R 61 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6757 (mt) REVERT: R 92 MET cc_start: 0.7828 (mmm) cc_final: 0.7329 (mmt) REVERT: R 143 ASP cc_start: 0.7887 (t70) cc_final: 0.6962 (t70) REVERT: R 356 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.5683 (mt) REVERT: R 385 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7120 (tp) outliers start: 34 outliers final: 18 residues processed: 173 average time/residue: 0.0710 time to fit residues: 16.8938 Evaluate side-chains 166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 331 ASN R 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.203615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175794 restraints weight = 7902.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.180380 restraints weight = 4553.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183564 restraints weight = 3109.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.185561 restraints weight = 2378.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.187165 restraints weight = 1983.645| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6878 Z= 0.127 Angle : 0.602 9.185 9336 Z= 0.310 Chirality : 0.041 0.166 1085 Planarity : 0.003 0.044 1160 Dihedral : 8.062 92.152 1081 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.96 % Allowed : 20.71 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 845 helix: 2.04 (0.27), residues: 372 sheet: -0.36 (0.40), residues: 171 loop : -0.81 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 333 TYR 0.019 0.002 TYR A 287 PHE 0.008 0.001 PHE R 165 TRP 0.056 0.002 TRP R 125 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6876) covalent geometry : angle 0.60245 / 0.31 ( 9332) SS BOND : bond 0.00826 / 0.43 ( 2) SS BOND : angle 0.48889 / 0.24 ( 4) hydrogen bonds : bond 0.03347 / 2.29 ( 375) hydrogen bonds : angle 4.67892 / 3.30 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.255 Fit side-chains REVERT: A 33 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6142 (tt0) REVERT: A 243 MET cc_start: 0.6290 (tmm) cc_final: 0.5833 (tmm) REVERT: A 253 ILE cc_start: 0.8662 (tp) cc_final: 0.8407 (tt) REVERT: A 315 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6156 (p0) REVERT: A 345 LYS cc_start: 0.7139 (mttt) cc_final: 0.6529 (mtmm) REVERT: B 46 ARG cc_start: 0.5874 (mtm110) cc_final: 0.5105 (mmt180) REVERT: B 170 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: B 234 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.5893 (t80) REVERT: B 252 LEU cc_start: 0.8036 (tp) cc_final: 0.7555 (tp) REVERT: B 283 ARG cc_start: 0.5353 (tpt-90) cc_final: 0.3545 (tpt-90) REVERT: R 61 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6795 (mt) REVERT: R 92 MET cc_start: 0.7797 (mmm) cc_final: 0.7366 (mmt) REVERT: R 143 ASP cc_start: 0.8002 (t70) cc_final: 0.7139 (t0) REVERT: R 351 MET cc_start: 0.7352 (mmm) cc_final: 0.7103 (mmm) REVERT: R 356 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.5832 (mt) REVERT: R 385 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7239 (tp) outliers start: 35 outliers final: 23 residues processed: 172 average time/residue: 0.0816 time to fit residues: 18.7546 Evaluate side-chains 169 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 77 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN R 36 GLN R 126 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.178744 restraints weight = 7900.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.183406 restraints weight = 4551.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.186596 restraints weight = 3108.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.188782 restraints weight = 2383.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.190104 restraints weight = 1972.106| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6878 Z= 0.114 Angle : 0.583 7.953 9336 Z= 0.302 Chirality : 0.041 0.193 1085 Planarity : 0.003 0.047 1160 Dihedral : 7.734 79.310 1081 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.25 % Allowed : 21.13 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.30), residues: 845 helix: 1.97 (0.28), residues: 374 sheet: -0.22 (0.41), residues: 164 loop : -0.82 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 341 TYR 0.017 0.002 TYR R 73 PHE 0.007 0.001 PHE R 362 TRP 0.065 0.002 TRP R 125 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6876) covalent geometry : angle 0.58345 / 0.30 ( 9332) SS BOND : bond 0.00888 / 0.47 ( 2) SS BOND : angle 0.42647 / 0.20 ( 4) hydrogen bonds : bond 0.03296 / 2.23 ( 375) hydrogen bonds : angle 4.66864 / 3.30 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.248 Fit side-chains REVERT: A 33 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6099 (tt0) REVERT: A 243 MET cc_start: 0.6253 (tmm) cc_final: 0.5693 (tmm) REVERT: A 253 ILE cc_start: 0.8700 (tp) cc_final: 0.8441 (tt) REVERT: A 345 LYS cc_start: 0.7066 (mttt) cc_final: 0.6740 (mtmt) REVERT: B 46 ARG cc_start: 0.5715 (mtm110) cc_final: 0.5002 (mmt180) REVERT: B 111 TYR cc_start: 0.6785 (m-80) cc_final: 0.6406 (m-80) REVERT: B 170 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: B 188 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.6806 (mpp) REVERT: B 234 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.5835 (t80) REVERT: B 252 LEU cc_start: 0.8108 (tp) cc_final: 0.7707 (tp) REVERT: B 283 ARG cc_start: 0.5335 (tpt-90) cc_final: 0.3504 (tpt-90) REVERT: R 61 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6796 (mt) REVERT: R 92 MET cc_start: 0.7862 (mmm) cc_final: 0.7447 (mmt) REVERT: R 143 ASP cc_start: 0.7933 (t70) cc_final: 0.7235 (t0) REVERT: R 211 MET cc_start: 0.7459 (ttm) cc_final: 0.7049 (ttm) REVERT: R 356 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.5780 (mt) REVERT: R 385 ILE cc_start: 0.7523 (tp) cc_final: 0.7305 (tp) outliers start: 37 outliers final: 20 residues processed: 180 average time/residue: 0.0761 time to fit residues: 18.4458 Evaluate side-chains 165 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN R 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.206257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.179220 restraints weight = 7791.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183517 restraints weight = 4706.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.186502 restraints weight = 3316.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.188365 restraints weight = 2591.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.189895 restraints weight = 2195.337| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6878 Z= 0.120 Angle : 0.614 10.727 9336 Z= 0.321 Chirality : 0.042 0.185 1085 Planarity : 0.003 0.049 1160 Dihedral : 7.035 81.976 1081 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.11 % Allowed : 22.27 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.30), residues: 845 helix: 1.98 (0.27), residues: 373 sheet: -0.30 (0.40), residues: 169 loop : -0.72 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 341 TYR 0.021 0.001 TYR A 302 PHE 0.015 0.001 PHE B 278 TRP 0.080 0.002 TRP R 125 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6876) covalent geometry : angle 0.61376 / 0.32 ( 9332) SS BOND : bond 0.00701 / 0.37 ( 2) SS BOND : angle 0.63439 / 0.30 ( 4) hydrogen bonds : bond 0.03298 / 2.22 ( 375) hydrogen bonds : angle 4.72065 / 3.33 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.250 Fit side-chains REVERT: A 33 GLU cc_start: 0.6431 (mt-10) cc_final: 0.6150 (tt0) REVERT: A 47 ASN cc_start: 0.5518 (t0) cc_final: 0.5240 (t0) REVERT: A 187 THR cc_start: 0.7106 (m) cc_final: 0.6800 (m) REVERT: A 243 MET cc_start: 0.6088 (tmm) cc_final: 0.5672 (tmm) REVERT: A 253 ILE cc_start: 0.8701 (tp) cc_final: 0.8433 (tt) REVERT: A 345 LYS cc_start: 0.7093 (mttt) cc_final: 0.6747 (mtmt) REVERT: B 46 ARG cc_start: 0.5661 (mtm110) cc_final: 0.5000 (mmt180) REVERT: B 111 TYR cc_start: 0.6897 (m-80) cc_final: 0.6482 (m-80) REVERT: B 188 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7006 (mpp) REVERT: B 234 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.5848 (t80) REVERT: B 252 LEU cc_start: 0.8134 (tp) cc_final: 0.7776 (tp) REVERT: B 283 ARG cc_start: 0.5249 (tpt-90) cc_final: 0.3508 (tpt-90) REVERT: R 61 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6847 (mt) REVERT: R 92 MET cc_start: 0.7821 (mmm) cc_final: 0.7497 (mmt) REVERT: R 143 ASP cc_start: 0.7964 (t70) cc_final: 0.7310 (t0) REVERT: R 211 MET cc_start: 0.7423 (ttm) cc_final: 0.7014 (ttm) REVERT: R 356 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.5990 (mt) REVERT: R 385 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7314 (tp) outliers start: 29 outliers final: 20 residues processed: 170 average time/residue: 0.0743 time to fit residues: 17.1541 Evaluate side-chains 166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 82 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 51 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.209305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181813 restraints weight = 7855.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.186411 restraints weight = 4506.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189623 restraints weight = 3078.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191653 restraints weight = 2347.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.193111 restraints weight = 1962.059| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6878 Z= 0.113 Angle : 0.628 12.050 9336 Z= 0.319 Chirality : 0.041 0.222 1085 Planarity : 0.003 0.050 1160 Dihedral : 6.409 84.715 1081 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.69 % Allowed : 23.26 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 845 helix: 2.06 (0.28), residues: 374 sheet: -0.25 (0.40), residues: 169 loop : -0.60 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 341 TYR 0.019 0.001 TYR A 302 PHE 0.012 0.001 PHE B 278 TRP 0.080 0.002 TRP R 125 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6876) covalent geometry : angle 0.62810 / 0.32 ( 9332) SS BOND : bond 0.00530 / 0.28 ( 2) SS BOND : angle 0.39021 / 0.19 ( 4) hydrogen bonds : bond 0.03277 / 2.19 ( 375) hydrogen bonds : angle 4.66670 / 3.30 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.319 Fit side-chains REVERT: A 33 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6153 (tt0) REVERT: A 47 ASN cc_start: 0.5547 (t0) cc_final: 0.5254 (t0) REVERT: A 243 MET cc_start: 0.6102 (tmm) cc_final: 0.5678 (tmm) REVERT: A 253 ILE cc_start: 0.8690 (tp) cc_final: 0.8424 (tt) REVERT: A 345 LYS cc_start: 0.7005 (mttt) cc_final: 0.6765 (mtmt) REVERT: B 46 ARG cc_start: 0.5621 (mtm110) cc_final: 0.4972 (mmt180) REVERT: B 111 TYR cc_start: 0.6692 (m-80) cc_final: 0.6197 (m-80) REVERT: B 170 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: B 188 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7156 (mpp) REVERT: B 234 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5782 (t80) REVERT: B 283 ARG cc_start: 0.5120 (tpt-90) cc_final: 0.3335 (tpt-90) REVERT: R 67 LEU cc_start: 0.8727 (mt) cc_final: 0.8524 (mp) REVERT: R 92 MET cc_start: 0.7834 (mmm) cc_final: 0.7589 (mmt) REVERT: R 140 ASP cc_start: 0.7691 (t0) cc_final: 0.7072 (p0) REVERT: R 143 ASP cc_start: 0.7925 (t70) cc_final: 0.7634 (t0) REVERT: R 211 MET cc_start: 0.7348 (ttm) cc_final: 0.6967 (ttm) REVERT: R 341 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7145 (mtm110) REVERT: R 356 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.5922 (mt) REVERT: R 385 ILE cc_start: 0.7484 (tp) cc_final: 0.7273 (tp) outliers start: 26 outliers final: 15 residues processed: 173 average time/residue: 0.0750 time to fit residues: 17.7635 Evaluate side-chains 165 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 56 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN B 32 GLN B 230 ASN R 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.207235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.178953 restraints weight = 7932.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.183568 restraints weight = 4651.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.186705 restraints weight = 3219.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.188780 restraints weight = 2488.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.190355 restraints weight = 2084.445| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6878 Z= 0.131 Angle : 0.644 12.789 9336 Z= 0.333 Chirality : 0.043 0.259 1085 Planarity : 0.003 0.048 1160 Dihedral : 6.480 87.857 1081 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.69 % Allowed : 24.11 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 845 helix: 1.95 (0.27), residues: 374 sheet: -0.25 (0.40), residues: 169 loop : -0.68 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 341 TYR 0.022 0.001 TYR A 287 PHE 0.023 0.001 PHE B 199 TRP 0.079 0.003 TRP R 125 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6876) covalent geometry : angle 0.64419 / 0.33 ( 9332) SS BOND : bond 0.00815 / 0.43 ( 2) SS BOND : angle 0.65532 / 0.31 ( 4) hydrogen bonds : bond 0.03366 / 2.27 ( 375) hydrogen bonds : angle 4.70547 / 3.34 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.248 Fit side-chains REVERT: A 33 GLU cc_start: 0.6342 (mt-10) cc_final: 0.6048 (tt0) REVERT: A 47 ASN cc_start: 0.5550 (t0) cc_final: 0.5268 (t0) REVERT: A 243 MET cc_start: 0.6053 (tmm) cc_final: 0.5719 (tmm) REVERT: A 253 ILE cc_start: 0.8703 (tp) cc_final: 0.8474 (tt) REVERT: A 345 LYS cc_start: 0.7078 (mttt) cc_final: 0.6712 (mtmt) REVERT: B 46 ARG cc_start: 0.5651 (mtm110) cc_final: 0.5009 (mmt180) REVERT: B 111 TYR cc_start: 0.6855 (m-80) cc_final: 0.6453 (m-80) REVERT: B 188 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7199 (mpp) REVERT: B 234 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.5864 (t80) REVERT: B 283 ARG cc_start: 0.5152 (tpt-90) cc_final: 0.3471 (tpt-90) REVERT: R 92 MET cc_start: 0.7782 (mmm) cc_final: 0.7537 (mmt) REVERT: R 125 TRP cc_start: 0.8050 (m-10) cc_final: 0.7734 (m-10) REVERT: R 143 ASP cc_start: 0.8007 (t70) cc_final: 0.7358 (t0) REVERT: R 211 MET cc_start: 0.7407 (ttm) cc_final: 0.6960 (ttm) REVERT: R 341 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.7004 (ttp-110) REVERT: R 356 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6017 (mt) REVERT: R 385 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7240 (tp) outliers start: 26 outliers final: 18 residues processed: 157 average time/residue: 0.0805 time to fit residues: 16.9877 Evaluate side-chains 161 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.0170 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.193645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169203 restraints weight = 8026.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.172889 restraints weight = 4814.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175563 restraints weight = 3395.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.177078 restraints weight = 2645.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.178499 restraints weight = 2239.574| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6878 Z= 0.178 Angle : 0.719 12.780 9336 Z= 0.367 Chirality : 0.045 0.256 1085 Planarity : 0.004 0.047 1160 Dihedral : 6.787 89.589 1081 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.83 % Allowed : 24.11 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 845 helix: 1.84 (0.27), residues: 374 sheet: -0.35 (0.39), residues: 179 loop : -0.90 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 333 TYR 0.029 0.002 TYR A 302 PHE 0.021 0.002 PHE B 199 TRP 0.091 0.003 TRP R 125 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6876) covalent geometry : angle 0.71843 / 0.37 ( 9332) SS BOND : bond 0.01010 / 0.53 ( 2) SS BOND : angle 0.99547 / 0.47 ( 4) hydrogen bonds : bond 0.03768 / 2.56 ( 375) hydrogen bonds : angle 4.89752 / 3.48 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6140 (tt0) REVERT: A 243 MET cc_start: 0.6184 (tmm) cc_final: 0.5739 (tmm) REVERT: A 248 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7729 (mttt) REVERT: A 353 LEU cc_start: 0.7592 (mt) cc_final: 0.7112 (mt) REVERT: B 46 ARG cc_start: 0.6072 (mtm110) cc_final: 0.5492 (mtm180) REVERT: B 111 TYR cc_start: 0.6947 (m-80) cc_final: 0.6728 (m-80) REVERT: B 234 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6275 (t80) REVERT: B 283 ARG cc_start: 0.5408 (tpt-90) cc_final: 0.3584 (tpt-90) REVERT: R 92 MET cc_start: 0.7602 (mmm) cc_final: 0.7328 (mmt) REVERT: R 125 TRP cc_start: 0.8183 (m-10) cc_final: 0.7958 (m-10) REVERT: R 140 ASP cc_start: 0.7545 (t0) cc_final: 0.7149 (p0) REVERT: R 143 ASP cc_start: 0.8057 (t70) cc_final: 0.7700 (t0) REVERT: R 211 MET cc_start: 0.7481 (ttm) cc_final: 0.7100 (ttm) REVERT: R 341 ARG cc_start: 0.7605 (ttp-110) cc_final: 0.7169 (ttp-110) REVERT: R 356 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6149 (mt) outliers start: 27 outliers final: 22 residues processed: 162 average time/residue: 0.0768 time to fit residues: 16.4835 Evaluate side-chains 155 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 TYR Chi-restraints excluded: chain R residue 330 GLU Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.196833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172244 restraints weight = 7940.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175885 restraints weight = 4850.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.178605 restraints weight = 3434.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.180244 restraints weight = 2677.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.181704 restraints weight = 2265.639| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6878 Z= 0.138 Angle : 0.673 12.673 9336 Z= 0.346 Chirality : 0.044 0.245 1085 Planarity : 0.003 0.047 1160 Dihedral : 6.673 93.234 1081 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.40 % Allowed : 25.25 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.29), residues: 845 helix: 1.79 (0.27), residues: 374 sheet: -0.38 (0.39), residues: 179 loop : -0.88 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 341 TYR 0.023 0.002 TYR A 287 PHE 0.021 0.001 PHE B 199 TRP 0.083 0.003 TRP R 125 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6876) covalent geometry : angle 0.67292 / 0.35 ( 9332) SS BOND : bond 0.00761 / 0.40 ( 2) SS BOND : angle 0.69701 / 0.33 ( 4) hydrogen bonds : bond 0.03564 / 2.42 ( 375) hydrogen bonds : angle 4.77184 / 3.39 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.85 seconds wall clock time: 21 minutes 18.38 seconds (1278.38 seconds total)