Starting phenix.real_space_refine on Tue Feb 3 19:32:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149.map" model { file = "/net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ljh_63149/02_2026/9ljh_63149_neut.cif" } resolution = 2.73 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= 0.053 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 54 5.16 5 C 4322 2.51 5 N 956 2.21 5 O 1079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 6415 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: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Unusual residues: {'LBN': 1, 'PLM': 7, 'Y01': 4, 'ZWY': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 75 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 338 Unusual residues: {'LBN': 3, 'PLM': 7, 'Y01': 4, 'ZWY': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 97 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: 1.63, per 1000 atoms: 0.25 Number of scatterers: 6415 At special positions: 0 Unit cell: (68.85, 79.05, 95.2, 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 54 16.00 P 4 15.00 O 1079 8.00 N 956 7.00 C 4322 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: 0.75 Conformation dependent library (CDL) restraints added in 239.1 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1410 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.561A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 78 removed outlier: 3.589A pdb=" N THR A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 93 through 108 removed outlier: 4.115A pdb=" N CYS A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 106 " --> pdb=" O CYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.516A pdb=" N GLU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 138 " --> pdb=" O MET A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 173 through 201 removed outlier: 3.652A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Proline residue: A 184 - end of helix removed outlier: 3.670A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.977A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 238 " --> pdb=" O TRP A 234 " (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: 3.594A pdb=" N LYS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 4.042A 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: 3.660A pdb=" N SER A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 33 through 63 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 38 through 46 removed outlier: 3.559A pdb=" N ARG C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 78 removed outlier: 3.585A pdb=" N THR C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) 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: 3.615A pdb=" N THR C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 138 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 173 through 201 removed outlier: 3.680A pdb=" N GLY C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix removed outlier: 3.658A pdb=" N TYR C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.948A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS C 246 " --> pdb=" O GLN C 242 " (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: 4.041A 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: 3.664A pdb=" N SER C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 33 through 64 416 hydrogen bonds defined for protein. 1236 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: 0.91 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 913 1.31 - 1.44: 1567 1.44 - 1.57: 3861 1.57 - 1.69: 129 1.69 - 1.82: 85 Bond restraints: 6555 Sorted by residual: bond pdb=" CAI Y01 A 409 " pdb=" CAZ Y01 A 409 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 C 410 " pdb=" CAZ Y01 C 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 3.16e+02 bond pdb=" CAI Y01 A 412 " pdb=" CAZ Y01 A 412 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.16e+02 bond pdb=" CAI Y01 A 410 " pdb=" CAZ Y01 A 410 " ideal model delta sigma weight residual 1.332 1.687 -0.355 2.00e-02 2.50e+03 3.15e+02 ... (remaining 6550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.57: 8787 5.57 - 11.14: 89 11.14 - 16.71: 6 16.71 - 22.28: 0 22.28 - 27.85: 1 Bond angle restraints: 8883 Sorted by residual: angle pdb=" C13 LBN C 414 " pdb=" C10 LBN C 414 " pdb=" C7 LBN C 414 " ideal model delta sigma weight residual 113.24 85.39 27.85 3.00e+00 1.11e-01 8.62e+01 angle pdb=" O TRP A 234 " pdb=" C TRP A 234 " pdb=" N THR A 235 " ideal model delta sigma weight residual 122.07 115.93 6.14 1.03e+00 9.43e-01 3.56e+01 angle pdb=" O1 LBN C 414 " pdb=" P1 LBN C 414 " pdb=" O2 LBN C 414 " ideal model delta sigma weight residual 93.45 109.84 -16.39 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CA TRP A 234 " pdb=" C TRP A 234 " pdb=" N THR A 235 " ideal model delta sigma weight residual 117.07 123.28 -6.21 1.14e+00 7.69e-01 2.96e+01 angle pdb=" C42 LBN C 414 " pdb=" C5 LBN C 414 " pdb=" C8 LBN C 414 " ideal model delta sigma weight residual 127.32 111.86 15.46 3.00e+00 1.11e-01 2.65e+01 ... (remaining 8878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 4229 35.89 - 71.78: 193 71.78 - 107.67: 33 107.67 - 143.57: 16 143.57 - 179.46: 4 Dihedral angle restraints: 4475 sinusoidal: 2300 harmonic: 2175 Sorted by residual: dihedral pdb=" O5 LBN C 414 " pdb=" C2 LBN C 414 " pdb=" C3 LBN C 414 " pdb=" O7 LBN C 414 " 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 4472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1028 0.121 - 0.243: 11 0.243 - 0.364: 18 0.364 - 0.486: 2 0.486 - 0.607: 8 Chirality restraints: 1067 Sorted by residual: chirality pdb=" CBI Y01 A 411 " pdb=" CAU Y01 A 411 " pdb=" CBE Y01 A 411 " pdb=" CBG Y01 A 411 " both_signs ideal model delta sigma weight residual False 2.94 2.33 0.61 2.00e-01 2.50e+01 9.22e+00 chirality pdb=" CBI Y01 C 412 " pdb=" CAU Y01 C 412 " pdb=" CBE Y01 C 412 " pdb=" CBG Y01 C 412 " both_signs ideal model delta sigma weight residual False 2.94 2.33 0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" CBI Y01 A 412 " pdb=" CAU Y01 A 412 " pdb=" CBE Y01 A 412 " pdb=" CBG Y01 A 412 " both_signs ideal model delta sigma weight residual False 2.94 2.34 0.60 2.00e-01 2.50e+01 8.87e+00 ... (remaining 1064 not shown) Planarity restraints: 1001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A 413 " 0.095 2.00e-02 2.50e+03 1.28e-01 2.05e+02 pdb=" C13 ZWY A 413 " -0.180 2.00e-02 2.50e+03 pdb=" C14 ZWY A 413 " 0.178 2.00e-02 2.50e+03 pdb=" C15 ZWY A 413 " -0.095 2.00e-02 2.50e+03 pdb=" C19 ZWY A 413 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 ZWY C 415 " -0.073 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" C13 ZWY C 415 " 0.153 2.00e-02 2.50e+03 pdb=" C14 ZWY C 415 " -0.180 2.00e-02 2.50e+03 pdb=" C15 ZWY C 415 " 0.088 2.00e-02 2.50e+03 pdb=" C19 ZWY C 415 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 414 " 0.026 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C42 LBN C 414 " -0.026 2.00e-02 2.50e+03 pdb=" C5 LBN C 414 " -0.025 2.00e-02 2.50e+03 pdb=" C8 LBN C 414 " 0.026 2.00e-02 2.50e+03 ... (remaining 998 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2136 2.87 - 3.38: 6026 3.38 - 3.89: 9900 3.89 - 4.39: 11398 4.39 - 4.90: 19774 Nonbonded interactions: 49234 Sorted by model distance: nonbonded pdb=" C3 PLM A 404 " pdb=" O2 PLM A 404 " model vdw 2.369 2.752 nonbonded pdb=" NH1 ARG A 86 " pdb=" C1 LBN A 408 " model vdw 2.411 3.520 nonbonded pdb=" OG SER A 289 " pdb=" N SER A 290 " model vdw 2.438 3.120 nonbonded pdb=" OG SER C 289 " pdb=" N SER C 290 " model vdw 2.444 3.120 nonbonded pdb=" O LEU A 302 " pdb=" OG1 THR A 306 " model vdw 2.468 3.040 ... (remaining 49229 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 404 or (resid 405 through 406 and (name C1 or na \ me C2 or name C3 or name C4 or name C5 or name C6 or name O2 )) or (resid 407 an \ d (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 or name O2 )) 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 n \ ame C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 4 or name C40 or name C41 or name C42 or name C6 or name C7 or name C9 or name N \ 1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 o \ r name O8 or name P1 )) or (resid 410 through 412 and (name CAA or name CAB or n \ ame 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 n \ ame 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 329 or (resid 401 and (name C1 or name C2 or nam \ e C3 or name C4 or name C5 or name C6 or name C7 or name O2 )) or (resid 402 thr \ ough 403 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or \ name C7 or name C8 or name O2 )) or resid 404 through 408 or resid 410 through 4 \ 12)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 16 through 63) } 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: 1.910 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.940 Find NCS groups from input model: 0.110 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.023 0.577 6572 Z= 1.344 Angle : 1.234 27.846 8887 Z= 0.528 Chirality : 0.080 0.607 1067 Planarity : 0.007 0.128 1001 Dihedral : 21.512 179.457 3059 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.31 % Allowed : 14.13 % Favored : 85.56 % 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: 2.19 (0.30), residues: 737 helix: 2.00 (0.21), residues: 557 sheet: None (None), residues: 0 loop : -0.23 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 241 TYR 0.014 0.001 TYR C 123 PHE 0.018 0.001 PHE C 127 TRP 0.006 0.001 TRP C 107 HIS 0.006 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.02219 ( 6555) covalent geometry : angle 1.23394 ( 8883) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.34436 ( 4) hydrogen bonds : bond 0.18096 ( 416) hydrogen bonds : angle 4.73705 ( 1236) Misc. bond : bond 0.15551 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.250 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.7659 time to fit residues: 66.8120 Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL 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: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 78 ASN C 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113959 restraints weight = 6242.234| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.32 r_work: 0.3062 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6572 Z= 0.154 Angle : 0.607 6.193 8887 Z= 0.289 Chirality : 0.039 0.125 1067 Planarity : 0.004 0.042 1001 Dihedral : 16.666 159.678 1699 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.84 % Allowed : 13.82 % Favored : 84.33 % 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: 737 helix: 2.43 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.25 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.016 0.002 TYR C 123 PHE 0.019 0.002 PHE C 127 TRP 0.008 0.001 TRP C 107 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6555) covalent geometry : angle 0.60743 ( 8883) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.71152 ( 4) hydrogen bonds : bond 0.07635 ( 416) hydrogen bonds : angle 3.62143 ( 1236) Misc. bond : bond 0.00111 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.308 Fit side-chains REVERT: A 86 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7270 (ppt-90) REVERT: B 34 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7512 (m) REVERT: C 50 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 116 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8055 (mt-10) outliers start: 12 outliers final: 3 residues processed: 85 average time/residue: 0.6464 time to fit residues: 57.3855 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.146216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112934 restraints weight = 6165.022| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.33 r_work: 0.3048 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6572 Z= 0.139 Angle : 0.541 7.099 8887 Z= 0.262 Chirality : 0.037 0.136 1067 Planarity : 0.004 0.035 1001 Dihedral : 15.086 155.567 1699 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 1.69 % Allowed : 14.59 % Favored : 83.72 % 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: 3.20 (0.31), residues: 737 helix: 2.71 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.31 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.014 0.002 TYR C 123 PHE 0.019 0.002 PHE C 127 TRP 0.006 0.001 TRP C 107 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6555) covalent geometry : angle 0.54051 ( 8883) SS BOND : bond 0.00316 ( 2) SS BOND : angle 0.69145 ( 4) hydrogen bonds : bond 0.07232 ( 416) hydrogen bonds : angle 3.45373 ( 1236) Misc. bond : bond 0.00065 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.208 Fit side-chains REVERT: A 86 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7427 (ppt-90) REVERT: C 116 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 176 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7570 (mttt) outliers start: 11 outliers final: 3 residues processed: 82 average time/residue: 0.6834 time to fit residues: 58.2054 Evaluate side-chains 74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 222 ASN 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 = 0.3633 r_free = 0.3633 target = 0.148179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115093 restraints weight = 6244.306| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.33 r_work: 0.3098 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6572 Z= 0.119 Angle : 0.508 8.978 8887 Z= 0.243 Chirality : 0.036 0.122 1067 Planarity : 0.004 0.031 1001 Dihedral : 14.099 153.798 1699 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.38 % Allowed : 14.59 % Favored : 84.02 % 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: 3.46 (0.31), residues: 737 helix: 2.89 (0.21), residues: 551 sheet: None (None), residues: 0 loop : 0.40 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.016 0.001 TYR C 123 PHE 0.017 0.001 PHE C 127 TRP 0.005 0.001 TRP B 26 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6555) covalent geometry : angle 0.50759 ( 8883) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.43936 ( 4) hydrogen bonds : bond 0.06182 ( 416) hydrogen bonds : angle 3.32728 ( 1236) Misc. bond : bond 0.00029 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.223 Fit side-chains REVERT: A 86 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7323 (ppt-90) REVERT: C 116 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7925 (mt-10) REVERT: C 176 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7522 (mttt) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.6752 time to fit residues: 58.3268 Evaluate side-chains 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 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 C 300 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110435 restraints weight = 6225.684| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.33 r_work: 0.3025 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6572 Z= 0.145 Angle : 0.545 6.051 8887 Z= 0.265 Chirality : 0.037 0.120 1067 Planarity : 0.004 0.031 1001 Dihedral : 13.134 153.510 1699 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 1.69 % Allowed : 14.59 % Favored : 83.72 % 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: 3.29 (0.30), residues: 737 helix: 2.80 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.25 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 241 TYR 0.015 0.002 TYR C 123 PHE 0.021 0.002 PHE C 127 TRP 0.004 0.001 TRP C 220 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6555) covalent geometry : angle 0.54509 ( 8883) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.73970 ( 4) hydrogen bonds : bond 0.07428 ( 416) hydrogen bonds : angle 3.42320 ( 1236) Misc. bond : bond 0.00046 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.234 Fit side-chains REVERT: A 86 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7563 (ppt-90) REVERT: C 116 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8013 (mt-10) REVERT: C 176 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7693 (mttt) outliers start: 11 outliers final: 2 residues processed: 83 average time/residue: 0.7008 time to fit residues: 60.6108 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.144892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112092 restraints weight = 6168.117| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.27 r_work: 0.3046 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6572 Z= 0.131 Angle : 0.505 5.803 8887 Z= 0.249 Chirality : 0.036 0.119 1067 Planarity : 0.004 0.027 1001 Dihedral : 12.719 154.848 1698 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.23 % Allowed : 14.90 % Favored : 83.87 % 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: 3.31 (0.30), residues: 737 helix: 2.83 (0.21), residues: 547 sheet: None (None), residues: 0 loop : 0.26 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.016 0.002 TYR C 123 PHE 0.020 0.001 PHE C 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 0.00255 ( 6555) covalent geometry : angle 0.50483 ( 8883) SS BOND : bond 0.00310 ( 2) SS BOND : angle 0.58290 ( 4) hydrogen bonds : bond 0.06838 ( 416) hydrogen bonds : angle 3.39092 ( 1236) Misc. bond : bond 0.00040 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7471 (ppt-90) REVERT: C 176 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7599 (mttt) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.7308 time to fit residues: 61.6370 Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.143176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107863 restraints weight = 5996.339| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.37 r_work: 0.3132 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6572 Z= 0.138 Angle : 0.514 5.937 8887 Z= 0.258 Chirality : 0.036 0.120 1067 Planarity : 0.004 0.028 1001 Dihedral : 12.615 155.292 1698 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.08 % Allowed : 14.90 % Favored : 84.02 % 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: 3.25 (0.30), residues: 737 helix: 2.80 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.15 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.015 0.002 TYR C 123 PHE 0.022 0.002 PHE C 127 TRP 0.005 0.001 TRP C 220 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6555) covalent geometry : angle 0.51373 ( 8883) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.68731 ( 4) hydrogen bonds : bond 0.07171 ( 416) hydrogen bonds : angle 3.41091 ( 1236) Misc. bond : bond 0.00041 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7582 (ppt-90) REVERT: C 176 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7687 (mttt) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.7436 time to fit residues: 60.2957 Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103967 restraints weight = 6044.649| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.38 r_work: 0.2969 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6572 Z= 0.174 Angle : 0.577 6.391 8887 Z= 0.289 Chirality : 0.039 0.127 1067 Planarity : 0.005 0.030 1001 Dihedral : 12.977 154.962 1698 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.54 % Allowed : 14.59 % Favored : 83.87 % 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: 2.86 (0.30), residues: 737 helix: 2.54 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.015 0.002 TYR C 123 PHE 0.024 0.002 PHE C 127 TRP 0.005 0.001 TRP C 220 HIS 0.008 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6555) covalent geometry : angle 0.57667 ( 8883) SS BOND : bond 0.00458 ( 2) SS BOND : angle 0.95935 ( 4) hydrogen bonds : bond 0.08624 ( 416) hydrogen bonds : angle 3.58850 ( 1236) Misc. bond : bond 0.00057 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.236 Fit side-chains REVERT: A 86 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7647 (ppt-90) REVERT: B 34 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7828 (m) REVERT: C 176 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7813 (mttt) REVERT: C 222 ASN cc_start: 0.7983 (m110) cc_final: 0.7681 (m-40) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.7445 time to fit residues: 61.9106 Evaluate side-chains 80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.144285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110659 restraints weight = 6267.342| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.32 r_work: 0.3133 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6572 Z= 0.131 Angle : 0.498 5.805 8887 Z= 0.250 Chirality : 0.036 0.120 1067 Planarity : 0.005 0.071 1001 Dihedral : 12.548 157.322 1698 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.77 % Allowed : 14.90 % Favored : 84.33 % 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: 3.19 (0.30), residues: 737 helix: 2.77 (0.21), residues: 547 sheet: None (None), residues: 0 loop : 0.10 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 241 TYR 0.015 0.001 TYR C 123 PHE 0.022 0.001 PHE C 127 TRP 0.006 0.001 TRP D 26 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6555) covalent geometry : angle 0.49772 ( 8883) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.54003 ( 4) hydrogen bonds : bond 0.06894 ( 416) hydrogen bonds : angle 3.44974 ( 1236) Misc. bond : bond 0.00042 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.239 Fit side-chains REVERT: A 86 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7559 (ppt-90) REVERT: C 176 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7665 (mttt) outliers start: 5 outliers final: 2 residues processed: 77 average time/residue: 0.7784 time to fit residues: 62.2874 Evaluate side-chains 74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.144611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111739 restraints weight = 6099.486| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.26 r_work: 0.3138 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6572 Z= 0.132 Angle : 0.499 5.830 8887 Z= 0.250 Chirality : 0.036 0.119 1067 Planarity : 0.004 0.055 1001 Dihedral : 12.319 157.657 1698 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.77 % Allowed : 15.36 % Favored : 83.87 % 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: 3.23 (0.30), residues: 737 helix: 2.78 (0.21), residues: 549 sheet: None (None), residues: 0 loop : 0.16 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.016 0.002 TYR C 123 PHE 0.021 0.001 PHE C 127 TRP 0.005 0.001 TRP C 220 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6555) covalent geometry : angle 0.49863 ( 8883) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.63222 ( 4) hydrogen bonds : bond 0.06925 ( 416) hydrogen bonds : angle 3.41066 ( 1236) Misc. bond : bond 0.00036 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.244 Fit side-chains REVERT: A 86 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7558 (ppt-90) REVERT: C 176 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7606 (mttt) outliers start: 5 outliers final: 1 residues processed: 76 average time/residue: 0.7791 time to fit residues: 61.5569 Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 27 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.2172 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.152303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120093 restraints weight = 6160.013| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.27 r_work: 0.3170 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6572 Z= 0.104 Angle : 0.441 5.268 8887 Z= 0.220 Chirality : 0.034 0.122 1067 Planarity : 0.004 0.047 1001 Dihedral : 11.653 160.696 1697 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.46 % Allowed : 15.98 % Favored : 83.56 % 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: 3.60 (0.31), residues: 737 helix: 3.05 (0.21), residues: 551 sheet: None (None), residues: 0 loop : 0.26 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 146 TYR 0.017 0.001 TYR C 123 PHE 0.016 0.001 PHE C 127 TRP 0.007 0.001 TRP D 26 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 6555) covalent geometry : angle 0.44073 ( 8883) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.12342 ( 4) hydrogen bonds : bond 0.05037 ( 416) hydrogen bonds : angle 3.20482 ( 1236) Misc. bond : bond 0.00020 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.29 seconds wall clock time: 39 minutes 46.11 seconds (2386.11 seconds total)