Starting phenix.real_space_refine on Tue Feb 3 19:41:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148.map" model { file = "/net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ljg_63148/02_2026/9ljg_63148_neut.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.122 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 4 5.49 5 S 52 5.16 5 C 4352 2.51 5 N 958 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2522 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 305} Chain: "B" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2522 Classifications: {'peptide': 324} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 305} Chain: "D" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Unusual residues: {'LBN': 1, 'PLM': 7, 'Y01': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'PLM:plan-1': 7, 'Y01:plan-1': 3, 'Y01:plan-2': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 347 Unusual residues: {'LBN': 3, 'PLM': 7, 'Y01': 5} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'PLM:plan-1': 7, 'LBN:plan-3': 2, 'Y01:plan-1': 3, 'Y01:plan-2': 3} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 1.64, per 1000 atoms: 0.25 Number of scatterers: 6444 At special positions: 0 Unit cell: (70.55, 79.05, 94.35, 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 52 16.00 P 4 15.00 O 1078 8.00 N 958 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 284 " 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 153.8 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 47 through 78 removed outlier: 3.575A pdb=" N TYR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.509A pdb=" N THR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.955A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 173 through 201 removed outlier: 3.656A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Proline residue: A 184 - end of helix removed outlier: 3.699A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.821A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.054A pdb=" N GLN A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 318 removed outlier: 3.805A pdb=" N SER A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 removed outlier: 3.553A pdb=" N LEU B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 64 Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 47 through 78 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.955A pdb=" N VAL C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 138 " --> pdb=" O MET C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 173 through 201 removed outlier: 3.651A pdb=" N GLY C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix removed outlier: 3.680A pdb=" N TYR C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.828A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 251 through 280 removed outlier: 4.043A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 289 through 318 removed outlier: 3.765A pdb=" N SER C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.562A pdb=" N LEU D 21 " --> pdb=" O PRO D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 64 424 hydrogen bonds defined for protein. 1260 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: 0.61 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 919 1.31 - 1.44: 1570 1.44 - 1.57: 3881 1.57 - 1.70: 138 1.70 - 1.83: 76 Bond restraints: 6584 Sorted by residual: bond pdb=" CAI Y01 C 410 " pdb=" CAZ Y01 C 410 " ideal model delta sigma weight residual 1.332 1.691 -0.359 2.00e-02 2.50e+03 3.23e+02 bond pdb=" CAI Y01 A 409 " pdb=" CAZ Y01 A 409 " ideal model delta sigma weight residual 1.332 1.690 -0.358 2.00e-02 2.50e+03 3.21e+02 bond pdb=" CAI Y01 C 413 " pdb=" CAZ Y01 C 413 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CAI Y01 A 410 " pdb=" CAZ Y01 A 410 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CAI Y01 C 411 " pdb=" CAZ Y01 C 411 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.17e+02 ... (remaining 6579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.57: 8795 5.57 - 11.14: 115 11.14 - 16.71: 4 16.71 - 22.28: 1 22.28 - 27.85: 1 Bond angle restraints: 8916 Sorted by residual: angle pdb=" C13 LBN C 415 " pdb=" C10 LBN C 415 " pdb=" C7 LBN C 415 " ideal model delta sigma weight residual 113.24 85.39 27.85 3.00e+00 1.11e-01 8.62e+01 angle pdb=" C ASP A 11 " pdb=" N PRO A 12 " pdb=" CA PRO A 12 " ideal model delta sigma weight residual 119.84 128.01 -8.17 1.25e+00 6.40e-01 4.27e+01 angle pdb=" C2 PLM C 402 " pdb=" C1 PLM C 402 " pdb=" O2 PLM C 402 " ideal model delta sigma weight residual 117.18 99.14 18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" N PHE A 104 " pdb=" CA PHE A 104 " pdb=" C PHE A 104 " ideal model delta sigma weight residual 111.07 104.65 6.42 1.07e+00 8.73e-01 3.60e+01 angle pdb=" C SER A 285 " pdb=" N PRO A 286 " pdb=" CA PRO A 286 " ideal model delta sigma weight residual 120.38 126.33 -5.95 1.03e+00 9.43e-01 3.34e+01 ... (remaining 8911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 4296 35.89 - 71.78: 160 71.78 - 107.67: 28 107.67 - 143.57: 14 143.57 - 179.46: 4 Dihedral angle restraints: 4502 sinusoidal: 2324 harmonic: 2178 Sorted by residual: dihedral pdb=" O5 LBN C 415 " pdb=" C2 LBN C 415 " pdb=" C3 LBN C 415 " pdb=" O7 LBN C 415 " ideal model delta sinusoidal sigma weight residual 62.67 -116.79 179.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 408 " pdb=" C2 LBN A 408 " pdb=" C3 LBN A 408 " pdb=" O7 LBN A 408 " ideal model delta sinusoidal sigma weight residual 62.67 -90.67 153.34 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C1 LBN C 409 " pdb=" O1 LBN C 409 " pdb=" P1 LBN C 409 " pdb=" O3 LBN C 409 " ideal model delta sinusoidal sigma weight residual -84.60 66.97 -151.57 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 4499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1027 0.130 - 0.259: 14 0.259 - 0.389: 17 0.389 - 0.518: 4 0.518 - 0.648: 10 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CBI Y01 C 410 " pdb=" CAU Y01 C 410 " pdb=" CBE Y01 C 410 " pdb=" CBG Y01 C 410 " both_signs ideal model delta sigma weight residual False 2.94 2.29 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CBI Y01 A 409 " pdb=" CAU Y01 A 409 " pdb=" CBE Y01 A 409 " pdb=" CBG Y01 A 409 " both_signs ideal model delta sigma weight residual False 2.94 2.29 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CBI Y01 C 413 " pdb=" CAU Y01 C 413 " pdb=" CBE Y01 C 413 " pdb=" CBG Y01 C 413 " both_signs ideal model delta sigma weight residual False 2.94 2.30 0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 1069 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 415 " 0.026 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C42 LBN C 415 " -0.026 2.00e-02 2.50e+03 pdb=" C5 LBN C 415 " -0.025 2.00e-02 2.50e+03 pdb=" C8 LBN C 415 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 163 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C CYS C 163 " 0.040 2.00e-02 2.50e+03 pdb=" O CYS C 163 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS C 164 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 17 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.56e+00 pdb=" C ASP A 17 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 17 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 18 " 0.012 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1214 2.78 - 3.31: 5961 3.31 - 3.84: 9860 3.84 - 4.37: 11687 4.37 - 4.90: 21042 Nonbonded interactions: 49764 Sorted by model distance: nonbonded pdb=" C3 PLM A 403 " pdb=" O2 PLM A 403 " model vdw 2.247 2.752 nonbonded pdb=" C3 PLM C 402 " pdb=" O2 PLM C 402 " model vdw 2.318 2.752 nonbonded pdb=" O LEU C 75 " pdb=" OG1 THR C 79 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" N1 LBN A 408 " model vdw 2.370 3.120 nonbonded pdb=" C3 PLM C 406 " pdb=" O2 PLM C 406 " model vdw 2.385 2.752 ... (remaining 49759 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 402 or (resid 403 and (name CA or name CB or nam \ e C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C \ 8 or name C9 or name O2 )) or (resid 404 and (name C1 or name C2 or name C3 or n \ ame C4 or name C5 or name C6 or name C7 or name C8 or name O2 )) or (resid 405 a \ nd (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name O2 )) \ or resid 406 through 407 or (resid 408 and (name C1 or name C10 or name C13 or \ name C16 or name C19 or name C2 or name C21 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C4 or name C40 or name C41 or name C42 or name C6 or name C7 or name C9 or na \ me N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name \ O7 or name O8 or name P1 )) or (resid 410 through 413 and (name CAA or name CAB \ or name CAC or name CAD or name CAE or name CAI or name CAJ or name CAK or name \ CAN or name CAO or name CAP or name CAQ or name CAR or name CAS or name CAT or n \ ame CAU or name CAV or name CAY or name CAZ or name CBA or name CBB or name CBC \ or name CBD or name CBE or name CBF or name CBG or name CBH or name CBI or name \ OAG or name OAW)))) selection = (chain 'C' and (resid 6 through 406 or (resid 407 and (name C1 or name C2 or nam \ e C3 or name C4 or name C5 or name C6 or name O2 )) or resid 408 or (resid 410 t \ hrough 413 and (name CAA or name CAB or name CAC or name CAD or name CAE or name \ CAI or name CAJ or name CAK or name CAN or name CAO or name CAP or name CAQ or \ name CAR or name CAS or name CAT or name CAU or name CAV or name CAY or name CAZ \ or name CBA or name CBB or name CBC or name CBD or name CBE or name CBF or name \ CBG or name CBH or name CBI or name OAG or name OAW)))) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.560 Find NCS groups from input model: 0.070 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.024 0.577 6601 Z= 1.353 Angle : 1.316 27.846 8920 Z= 0.552 Chirality : 0.088 0.648 1072 Planarity : 0.005 0.044 1002 Dihedral : 20.338 179.457 3084 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.07 % Allowed : 11.81 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.84 (0.31), residues: 738 helix: 2.52 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.26 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.009 0.001 TYR C 316 PHE 0.016 0.001 PHE A 104 TRP 0.005 0.001 TRP D 26 HIS 0.002 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.02247 ( 6584) covalent geometry : angle 1.31612 ( 8916) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.25337 ( 4) hydrogen bonds : bond 0.16121 ( 424) hydrogen bonds : angle 4.53996 ( 1260) Misc. bond : bond 0.15286 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.244 Fit side-chains REVERT: A 9 LYS cc_start: 0.7886 (mttt) cc_final: 0.7077 (mmtt) REVERT: A 77 LYS cc_start: 0.7405 (ttmt) cc_final: 0.7135 (ttmm) outliers start: 7 outliers final: 3 residues processed: 93 average time/residue: 0.6593 time to fit residues: 63.8139 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111794 restraints weight = 6934.131| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.62 r_work: 0.3169 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6601 Z= 0.145 Angle : 0.626 8.912 8920 Z= 0.285 Chirality : 0.041 0.214 1072 Planarity : 0.004 0.026 1002 Dihedral : 16.384 160.304 1721 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.53 % Allowed : 13.04 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.44 (0.31), residues: 738 helix: 3.00 (0.21), residues: 548 sheet: None (None), residues: 0 loop : 0.03 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.009 0.001 TYR A 316 PHE 0.014 0.001 PHE A 127 TRP 0.005 0.001 TRP D 26 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6584) covalent geometry : angle 0.62561 ( 8916) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.68563 ( 4) hydrogen bonds : bond 0.07104 ( 424) hydrogen bonds : angle 3.58584 ( 1260) Misc. bond : bond 0.00056 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8100 (mttt) cc_final: 0.7306 (mmtt) REVERT: A 23 LYS cc_start: 0.7190 (mttt) cc_final: 0.6887 (tmtt) REVERT: A 77 LYS cc_start: 0.7395 (ttmt) cc_final: 0.7172 (ttmm) REVERT: A 211 ASP cc_start: 0.6960 (t0) cc_final: 0.6755 (t0) REVERT: A 214 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: C 211 ASP cc_start: 0.6934 (t0) cc_final: 0.6710 (t0) outliers start: 10 outliers final: 2 residues processed: 87 average time/residue: 0.7033 time to fit residues: 63.5825 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 214 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108079 restraints weight = 6908.822| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.55 r_work: 0.3155 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6601 Z= 0.153 Angle : 0.570 7.331 8920 Z= 0.271 Chirality : 0.039 0.192 1072 Planarity : 0.004 0.028 1002 Dihedral : 14.594 156.821 1719 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.23 % Allowed : 13.65 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.63 (0.30), residues: 738 helix: 3.13 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.012 0.001 TYR A 74 PHE 0.013 0.002 PHE C 68 TRP 0.005 0.001 TRP D 26 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6584) covalent geometry : angle 0.57031 ( 8916) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.82992 ( 4) hydrogen bonds : bond 0.07471 ( 424) hydrogen bonds : angle 3.47269 ( 1260) Misc. bond : bond 0.00079 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8200 (mttt) cc_final: 0.7396 (mmtt) REVERT: A 23 LYS cc_start: 0.7247 (mttt) cc_final: 0.6936 (tmtt) REVERT: A 77 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7298 (ttmm) REVERT: A 211 ASP cc_start: 0.7012 (t0) cc_final: 0.6772 (t0) REVERT: A 214 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: B 52 MET cc_start: 0.7295 (mmp) cc_final: 0.7063 (mmp) REVERT: C 211 ASP cc_start: 0.6954 (t0) cc_final: 0.6708 (t0) REVERT: C 214 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7389 (pt0) outliers start: 8 outliers final: 2 residues processed: 85 average time/residue: 0.6122 time to fit residues: 54.1144 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 214 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111295 restraints weight = 6858.736| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.60 r_work: 0.3170 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6601 Z= 0.128 Angle : 0.512 7.313 8920 Z= 0.246 Chirality : 0.038 0.211 1072 Planarity : 0.004 0.026 1002 Dihedral : 13.866 155.497 1718 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.23 % Allowed : 13.96 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.81 (0.31), residues: 738 helix: 3.29 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.03 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.009 0.001 TYR A 74 PHE 0.011 0.001 PHE A 127 TRP 0.005 0.001 TRP D 26 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6584) covalent geometry : angle 0.51218 ( 8916) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.58614 ( 4) hydrogen bonds : bond 0.06450 ( 424) hydrogen bonds : angle 3.33850 ( 1260) Misc. bond : bond 0.00035 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8192 (mttt) cc_final: 0.7365 (mmtt) REVERT: A 23 LYS cc_start: 0.7232 (mttt) cc_final: 0.6988 (tmtt) REVERT: A 77 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7305 (ttmm) REVERT: A 211 ASP cc_start: 0.7073 (t0) cc_final: 0.6798 (t0) REVERT: A 214 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: A 309 MET cc_start: 0.7863 (mmp) cc_final: 0.7508 (mmp) REVERT: C 211 ASP cc_start: 0.7027 (t0) cc_final: 0.6738 (t0) REVERT: C 214 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7391 (pt0) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.5454 time to fit residues: 51.1855 Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 214 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 300 HIS C 178 GLN C 300 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112850 restraints weight = 6809.151| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.59 r_work: 0.3198 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6601 Z= 0.120 Angle : 0.495 7.951 8920 Z= 0.238 Chirality : 0.037 0.201 1072 Planarity : 0.004 0.026 1002 Dihedral : 13.425 155.258 1718 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.46 % Allowed : 15.03 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.92 (0.31), residues: 738 helix: 3.32 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.00 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.008 0.001 TYR A 74 PHE 0.010 0.001 PHE C 68 TRP 0.005 0.001 TRP D 26 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6584) covalent geometry : angle 0.49492 ( 8916) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.48466 ( 4) hydrogen bonds : bond 0.05989 ( 424) hydrogen bonds : angle 3.22260 ( 1260) Misc. bond : bond 0.00036 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8195 (mttt) cc_final: 0.7291 (mmtt) REVERT: A 23 LYS cc_start: 0.7111 (mttt) cc_final: 0.6887 (tmtt) REVERT: A 77 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7231 (ttmm) REVERT: A 211 ASP cc_start: 0.7017 (t0) cc_final: 0.6735 (t0) REVERT: A 214 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: C 211 ASP cc_start: 0.6956 (t0) cc_final: 0.6685 (t0) outliers start: 3 outliers final: 2 residues processed: 95 average time/residue: 0.5692 time to fit residues: 56.4198 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 175 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 0.7734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104692 restraints weight = 6676.352| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.64 r_work: 0.3081 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6601 Z= 0.126 Angle : 0.501 7.811 8920 Z= 0.242 Chirality : 0.037 0.220 1072 Planarity : 0.004 0.030 1002 Dihedral : 13.349 155.242 1718 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.23 % Allowed : 15.03 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.87 (0.31), residues: 738 helix: 3.30 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.10 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.010 0.001 TYR A 74 PHE 0.011 0.001 PHE A 127 TRP 0.004 0.001 TRP B 26 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6584) covalent geometry : angle 0.50104 ( 8916) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.60418 ( 4) hydrogen bonds : bond 0.06318 ( 424) hydrogen bonds : angle 3.23603 ( 1260) Misc. bond : bond 0.00039 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8206 (mttt) cc_final: 0.7306 (mmtt) REVERT: A 23 LYS cc_start: 0.7186 (mttt) cc_final: 0.6984 (tmtt) REVERT: A 77 LYS cc_start: 0.7608 (ttmt) cc_final: 0.7363 (ttmm) REVERT: A 211 ASP cc_start: 0.7126 (t0) cc_final: 0.6856 (t0) REVERT: C 211 ASP cc_start: 0.7082 (t0) cc_final: 0.6815 (t0) outliers start: 8 outliers final: 2 residues processed: 90 average time/residue: 0.5699 time to fit residues: 53.3817 Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 175 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110979 restraints weight = 6506.702| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.50 r_work: 0.3133 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6601 Z= 0.111 Angle : 0.473 7.890 8920 Z= 0.228 Chirality : 0.036 0.225 1072 Planarity : 0.004 0.027 1002 Dihedral : 13.015 155.265 1718 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.31 % Allowed : 16.26 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.01 (0.31), residues: 738 helix: 3.41 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.07 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.008 0.001 TYR A 74 PHE 0.009 0.001 PHE A 127 TRP 0.005 0.001 TRP D 26 HIS 0.002 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 6584) covalent geometry : angle 0.47321 ( 8916) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.40598 ( 4) hydrogen bonds : bond 0.05531 ( 424) hydrogen bonds : angle 3.13167 ( 1260) Misc. bond : bond 0.00024 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8216 (mttt) cc_final: 0.7320 (mmtt) REVERT: A 211 ASP cc_start: 0.7130 (t0) cc_final: 0.6857 (t0) REVERT: C 9 LYS cc_start: 0.8192 (mttt) cc_final: 0.7402 (mmtt) REVERT: C 211 ASP cc_start: 0.7132 (t0) cc_final: 0.6877 (t0) REVERT: C 241 ARG cc_start: 0.7585 (mmt-90) cc_final: 0.7377 (mmt-90) outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 0.5569 time to fit residues: 53.8490 Evaluate side-chains 89 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 175 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106053 restraints weight = 6590.053| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.59 r_work: 0.3100 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6601 Z= 0.122 Angle : 0.491 8.249 8920 Z= 0.236 Chirality : 0.036 0.222 1072 Planarity : 0.004 0.032 1002 Dihedral : 12.990 155.319 1718 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.46 % Allowed : 16.56 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.00 (0.31), residues: 738 helix: 3.40 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.09 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 13 TYR 0.010 0.001 TYR A 74 PHE 0.011 0.001 PHE A 127 TRP 0.004 0.001 TRP D 26 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6584) covalent geometry : angle 0.49121 ( 8916) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.56393 ( 4) hydrogen bonds : bond 0.06011 ( 424) hydrogen bonds : angle 3.16819 ( 1260) Misc. bond : bond 0.00034 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8213 (mttt) cc_final: 0.7320 (mmtt) REVERT: A 211 ASP cc_start: 0.7144 (t0) cc_final: 0.6879 (t0) REVERT: A 241 ARG cc_start: 0.7958 (tpt170) cc_final: 0.7736 (tpt170) REVERT: C 211 ASP cc_start: 0.7161 (t0) cc_final: 0.6924 (t0) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.5384 time to fit residues: 50.4896 Evaluate side-chains 89 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 175 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111275 restraints weight = 7002.181| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.63 r_work: 0.3194 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6601 Z= 0.138 Angle : 0.520 8.294 8920 Z= 0.252 Chirality : 0.037 0.194 1072 Planarity : 0.004 0.029 1002 Dihedral : 13.105 155.190 1718 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.77 % Allowed : 16.41 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.94 (0.31), residues: 738 helix: 3.41 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -0.18 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 13 TYR 0.012 0.001 TYR A 74 PHE 0.012 0.001 PHE C 68 TRP 0.004 0.001 TRP D 26 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6584) covalent geometry : angle 0.52029 ( 8916) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.75239 ( 4) hydrogen bonds : bond 0.06875 ( 424) hydrogen bonds : angle 3.27315 ( 1260) Misc. bond : bond 0.00042 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.181 Fit side-chains REVERT: A 9 LYS cc_start: 0.8171 (mttt) cc_final: 0.7262 (mmtt) REVERT: A 211 ASP cc_start: 0.7090 (t0) cc_final: 0.6801 (t0) REVERT: C 211 ASP cc_start: 0.7003 (t0) cc_final: 0.6727 (t0) REVERT: C 241 ARG cc_start: 0.7610 (mmt-90) cc_final: 0.7381 (mmt-90) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.5762 time to fit residues: 53.4448 Evaluate side-chains 90 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 64 optimal weight: 0.0470 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 41 GLN C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113643 restraints weight = 6839.652| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.60 r_work: 0.3230 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6601 Z= 0.115 Angle : 0.483 7.992 8920 Z= 0.233 Chirality : 0.036 0.192 1072 Planarity : 0.004 0.033 1002 Dihedral : 12.742 155.850 1718 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.31 % Allowed : 16.72 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.02 (0.31), residues: 738 helix: 3.43 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.15 (0.49), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 13 TYR 0.008 0.001 TYR A 74 PHE 0.010 0.001 PHE A 127 TRP 0.005 0.001 TRP D 26 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6584) covalent geometry : angle 0.48338 ( 8916) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.44422 ( 4) hydrogen bonds : bond 0.05747 ( 424) hydrogen bonds : angle 3.16189 ( 1260) Misc. bond : bond 0.00028 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8172 (mttt) cc_final: 0.7270 (mmtt) REVERT: A 211 ASP cc_start: 0.7004 (t0) cc_final: 0.6696 (t0) REVERT: C 9 LYS cc_start: 0.8183 (mttt) cc_final: 0.7331 (mmtt) REVERT: C 211 ASP cc_start: 0.7038 (t0) cc_final: 0.6770 (t0) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.6164 time to fit residues: 56.4937 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 175 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.0020 chunk 28 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112115 restraints weight = 6570.835| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.59 r_work: 0.3184 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6601 Z= 0.101 Angle : 0.460 7.582 8920 Z= 0.220 Chirality : 0.035 0.185 1072 Planarity : 0.004 0.035 1002 Dihedral : 12.136 156.824 1718 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.61 % Allowed : 16.56 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.09 (0.31), residues: 738 helix: 3.40 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.04 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 13 TYR 0.007 0.001 TYR A 123 PHE 0.008 0.001 PHE A 127 TRP 0.005 0.001 TRP D 26 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 6584) covalent geometry : angle 0.46037 ( 8916) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.18275 ( 4) hydrogen bonds : bond 0.04648 ( 424) hydrogen bonds : angle 2.99012 ( 1260) Misc. bond : bond 0.00020 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.80 seconds wall clock time: 34 minutes 48.54 seconds (2088.54 seconds total)