Starting phenix.real_space_refine on Tue Mar 3 20:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zd0_74047/03_2026/9zd0_74047.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.005 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 6 5.49 5 S 69 5.16 5 C 5577 2.51 5 N 1257 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8355 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2699 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8355 At special positions: 0 Unit cell: (100.793, 101.626, 73.304, 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 69 16.00 P 6 15.00 O 1446 8.00 N 1257 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 231.5 milliseconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 removed outlier: 3.626A pdb=" N TYR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.626A pdb=" N LYS A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 74 through 89 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 122 through 137 removed outlier: 4.573A pdb=" N ALA A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 171 removed outlier: 3.591A pdb=" N THR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 3.663A pdb=" N LYS A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TRP A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.716A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.606A pdb=" N SER A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 286 through 298 removed outlier: 4.353A pdb=" N SER A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 331 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 369 through 385 removed outlier: 3.535A pdb=" N ILE A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 383 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.629A pdb=" N TYR B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 3.887A pdb=" N LYS B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 74 through 89 removed outlier: 3.823A pdb=" N LEU B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 110 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.587A pdb=" N ALA B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 171 Proline residue: B 158 - end of helix removed outlier: 3.722A pdb=" N LYS B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.713A pdb=" N ILE B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.676A pdb=" N SER B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.311A pdb=" N SER B 290 " --> pdb=" O TRP B 286 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 331 Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.525A pdb=" N CYS B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.682A pdb=" N ARG B 383 " --> pdb=" O GLN B 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.606A pdb=" N TYR C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 52 removed outlier: 3.756A pdb=" N LYS C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 74 through 89 removed outlier: 3.723A pdb=" N LEU C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 110 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 122 through 136 removed outlier: 4.564A pdb=" N ALA C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 170 Proline residue: C 158 - end of helix removed outlier: 3.648A pdb=" N LYS C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.724A pdb=" N ILE C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.528A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 274 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'C' and resid 286 through 298 removed outlier: 4.315A pdb=" N SER C 290 " --> pdb=" O TRP C 286 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 331 Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.529A pdb=" N LYS C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 383 " --> pdb=" O GLN C 379 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1333 1.33 - 1.45: 2268 1.45 - 1.57: 4853 1.57 - 1.70: 12 1.70 - 1.82: 114 Bond restraints: 8580 Sorted by residual: bond pdb=" CB GLU A 332 " pdb=" CG GLU A 332 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB GLU C 332 " pdb=" CG GLU C 332 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB GLU B 332 " pdb=" CG GLU B 332 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CB GLN C 88 " pdb=" CG GLN C 88 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CB ASP B 60 " pdb=" CG ASP B 60 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.03e+00 ... (remaining 8575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11424 1.84 - 3.68: 193 3.68 - 5.52: 40 5.52 - 7.36: 11 7.36 - 9.21: 2 Bond angle restraints: 11670 Sorted by residual: angle pdb=" N VAL B 333 " pdb=" CA VAL B 333 " pdb=" C VAL B 333 " ideal model delta sigma weight residual 112.29 108.96 3.33 9.40e-01 1.13e+00 1.25e+01 angle pdb=" CB GLU A 332 " pdb=" CG GLU A 332 " pdb=" CD GLU A 332 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+01 angle pdb=" CB GLU C 332 " pdb=" CG GLU C 332 " pdb=" CD GLU C 332 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.70e+00 3.46e-01 1.16e+01 angle pdb=" N VAL A 333 " pdb=" CA VAL A 333 " pdb=" C VAL A 333 " ideal model delta sigma weight residual 112.29 109.09 3.20 9.40e-01 1.13e+00 1.16e+01 angle pdb=" N VAL C 333 " pdb=" CA VAL C 333 " pdb=" C VAL C 333 " ideal model delta sigma weight residual 112.29 109.12 3.17 9.40e-01 1.13e+00 1.14e+01 ... (remaining 11665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 4697 26.86 - 53.71: 290 53.71 - 80.57: 22 80.57 - 107.42: 1 107.42 - 134.28: 3 Dihedral angle restraints: 5013 sinusoidal: 1959 harmonic: 3054 Sorted by residual: dihedral pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " pdb=" P1 PTY A 401 " pdb=" O12 PTY A 401 " ideal model delta sinusoidal sigma weight residual 300.23 165.95 134.28 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" C3 PTY B 401 " pdb=" O11 PTY B 401 " pdb=" P1 PTY B 401 " pdb=" O12 PTY B 401 " ideal model delta sinusoidal sigma weight residual 300.23 168.24 131.99 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C3 PTY C 401 " pdb=" O11 PTY C 401 " pdb=" P1 PTY C 401 " pdb=" O12 PTY C 401 " ideal model delta sinusoidal sigma weight residual 300.23 172.05 128.18 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 5010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 937 0.033 - 0.065: 289 0.065 - 0.098: 94 0.098 - 0.131: 22 0.131 - 0.163: 2 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CB ILE C 81 " pdb=" CA ILE C 81 " pdb=" CG1 ILE C 81 " pdb=" CG2 ILE C 81 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CB ILE B 81 " pdb=" CA ILE B 81 " pdb=" CG1 ILE B 81 " pdb=" CG2 ILE B 81 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA PRO A 370 " pdb=" N PRO A 370 " pdb=" C PRO A 370 " pdb=" CB PRO A 370 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1341 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 339 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C THR A 339 " 0.026 2.00e-02 2.50e+03 pdb=" O THR A 339 " -0.010 2.00e-02 2.50e+03 pdb=" N TRP A 340 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 339 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C THR B 339 " 0.023 2.00e-02 2.50e+03 pdb=" O THR B 339 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP B 340 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 221 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" CD GLU A 221 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU A 221 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 221 " 0.008 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4000 2.98 - 3.46: 9310 3.46 - 3.94: 14892 3.94 - 4.42: 17818 4.42 - 4.90: 26582 Nonbonded interactions: 72602 Sorted by model distance: nonbonded pdb=" N GLU C 332 " pdb=" OE1 GLU C 332 " model vdw 2.496 3.120 nonbonded pdb=" O THR B 177 " pdb=" OG1 THR B 177 " model vdw 2.501 3.040 nonbonded pdb=" N GLU A 332 " pdb=" OE1 GLU A 332 " model vdw 2.502 3.120 nonbonded pdb=" N GLU B 332 " pdb=" OE1 GLU B 332 " model vdw 2.532 3.120 nonbonded pdb=" N VAL B 333 " pdb=" N GLY B 334 " model vdw 2.603 2.560 ... (remaining 72597 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8580 Z= 0.122 Angle : 0.623 9.205 11670 Z= 0.329 Chirality : 0.037 0.163 1344 Planarity : 0.004 0.026 1395 Dihedral : 16.281 134.281 3057 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.73 % Allowed : 23.18 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1059 helix: 1.42 (0.18), residues: 768 sheet: None (None), residues: 0 loop : 1.47 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.017 0.001 TYR B 369 PHE 0.009 0.001 PHE B 288 TRP 0.012 0.001 TRP B 340 HIS 0.001 0.000 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8580) covalent geometry : angle 0.62273 (11670) hydrogen bonds : bond 0.24208 ( 551) hydrogen bonds : angle 6.12157 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7154 (pt) REVERT: A 379 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: B 289 ASN cc_start: 0.9191 (m-40) cc_final: 0.8988 (m110) REVERT: B 371 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: B 379 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: C 177 THR cc_start: 0.9361 (p) cc_final: 0.8984 (t) REVERT: C 372 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8641 (mt-10) REVERT: C 375 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7184 (pt) REVERT: C 379 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7673 (mp10) outliers start: 15 outliers final: 6 residues processed: 144 average time/residue: 0.4658 time to fit residues: 72.1961 Evaluate side-chains 141 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 88 GLN C 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.086527 restraints weight = 17810.516| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.15 r_work: 0.3014 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8580 Z= 0.136 Angle : 0.573 5.846 11670 Z= 0.288 Chirality : 0.040 0.136 1344 Planarity : 0.004 0.045 1395 Dihedral : 12.214 131.380 1341 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.11 % Allowed : 19.61 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.26), residues: 1059 helix: 2.03 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 1.33 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.016 0.001 TYR A 369 PHE 0.009 0.001 PHE B 160 TRP 0.011 0.001 TRP A 306 HIS 0.001 0.000 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8580) covalent geometry : angle 0.57277 (11670) hydrogen bonds : bond 0.05446 ( 551) hydrogen bonds : angle 4.02222 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8387 (mtpt) REVERT: A 52 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5977 (mmtt) REVERT: A 204 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8926 (pp) REVERT: A 372 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 251 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 382 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8158 (pmtt) REVERT: C 81 ILE cc_start: 0.9373 (mp) cc_final: 0.9159 (mp) REVERT: C 237 ASP cc_start: 0.8949 (p0) cc_final: 0.8666 (p0) REVERT: C 362 MET cc_start: 0.8317 (mmm) cc_final: 0.8090 (mmm) outliers start: 27 outliers final: 12 residues processed: 169 average time/residue: 0.4105 time to fit residues: 75.1032 Evaluate side-chains 150 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 79 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 280 ASN C 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.087542 restraints weight = 17589.555| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.12 r_work: 0.3011 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8580 Z= 0.118 Angle : 0.541 6.369 11670 Z= 0.264 Chirality : 0.039 0.136 1344 Planarity : 0.004 0.042 1395 Dihedral : 11.858 128.011 1331 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.23 % Allowed : 20.30 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.26), residues: 1059 helix: 2.13 (0.18), residues: 786 sheet: None (None), residues: 0 loop : 1.19 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.013 0.001 TYR A 369 PHE 0.008 0.001 PHE A 288 TRP 0.008 0.001 TRP A 306 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8580) covalent geometry : angle 0.54147 (11670) hydrogen bonds : bond 0.04643 ( 551) hydrogen bonds : angle 3.67089 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8898 (pp) REVERT: A 302 MET cc_start: 0.8868 (mtp) cc_final: 0.8663 (mmt) REVERT: A 372 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8384 (mt-10) REVERT: B 39 THR cc_start: 0.8137 (t) cc_final: 0.7790 (m) REVERT: B 216 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: B 223 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8715 (tm) REVERT: B 251 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8253 (tp) REVERT: B 279 GLU cc_start: 0.8652 (mp0) cc_final: 0.8278 (pt0) REVERT: C 81 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9165 (mp) REVERT: C 362 MET cc_start: 0.8287 (mmm) cc_final: 0.7868 (mmm) REVERT: C 372 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8630 (mt-10) outliers start: 28 outliers final: 11 residues processed: 161 average time/residue: 0.4199 time to fit residues: 73.3253 Evaluate side-chains 146 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 0.2980 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.0030 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN C 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088808 restraints weight = 17906.393| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.14 r_work: 0.3036 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8580 Z= 0.109 Angle : 0.529 6.693 11670 Z= 0.258 Chirality : 0.038 0.135 1344 Planarity : 0.004 0.041 1395 Dihedral : 11.703 125.658 1331 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.69 % Allowed : 20.99 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.26), residues: 1059 helix: 2.23 (0.18), residues: 786 sheet: None (None), residues: 0 loop : 1.16 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 374 TYR 0.013 0.001 TYR A 369 PHE 0.007 0.001 PHE B 245 TRP 0.009 0.001 TRP B 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8580) covalent geometry : angle 0.52930 (11670) hydrogen bonds : bond 0.04208 ( 551) hydrogen bonds : angle 3.54485 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 39 THR cc_start: 0.8086 (t) cc_final: 0.7726 (m) REVERT: C 81 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9163 (mp) REVERT: C 237 ASP cc_start: 0.8797 (p0) cc_final: 0.8511 (p0) REVERT: C 251 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8219 (tp) REVERT: C 283 PHE cc_start: 0.8293 (m-80) cc_final: 0.7651 (t80) REVERT: C 362 MET cc_start: 0.8193 (mmm) cc_final: 0.7871 (mmm) REVERT: C 372 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8596 (mt-10) REVERT: C 375 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7666 (pt) outliers start: 32 outliers final: 9 residues processed: 162 average time/residue: 0.4276 time to fit residues: 75.0892 Evaluate side-chains 143 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088423 restraints weight = 17779.425| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.11 r_work: 0.3040 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8580 Z= 0.118 Angle : 0.551 7.477 11670 Z= 0.267 Chirality : 0.039 0.136 1344 Planarity : 0.004 0.041 1395 Dihedral : 11.340 122.618 1323 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.77 % Allowed : 22.03 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.26), residues: 1059 helix: 2.24 (0.18), residues: 786 sheet: None (None), residues: 0 loop : 1.26 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.012 0.001 TYR A 369 PHE 0.007 0.001 PHE A 288 TRP 0.007 0.001 TRP B 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8580) covalent geometry : angle 0.55107 (11670) hydrogen bonds : bond 0.04241 ( 551) hydrogen bonds : angle 3.54958 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8084 (m) REVERT: A 372 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8443 (mt-10) REVERT: B 39 THR cc_start: 0.8056 (t) cc_final: 0.7744 (m) REVERT: B 279 GLU cc_start: 0.8693 (mp0) cc_final: 0.8353 (pt0) REVERT: C 81 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9157 (mp) REVERT: C 268 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8082 (mp) REVERT: C 372 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8580 (mt-10) outliers start: 24 outliers final: 6 residues processed: 157 average time/residue: 0.4261 time to fit residues: 72.6120 Evaluate side-chains 147 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088299 restraints weight = 17902.297| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.13 r_work: 0.3027 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8580 Z= 0.115 Angle : 0.542 6.828 11670 Z= 0.265 Chirality : 0.039 0.134 1344 Planarity : 0.004 0.043 1395 Dihedral : 11.248 120.561 1322 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.42 % Allowed : 22.84 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.26), residues: 1059 helix: 2.26 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.27 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 374 TYR 0.013 0.001 TYR A 369 PHE 0.008 0.001 PHE B 245 TRP 0.009 0.001 TRP C 340 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8580) covalent geometry : angle 0.54235 (11670) hydrogen bonds : bond 0.04180 ( 551) hydrogen bonds : angle 3.53563 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8074 (m) REVERT: A 372 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8435 (mt-10) REVERT: B 39 THR cc_start: 0.8044 (t) cc_final: 0.7744 (m) REVERT: B 279 GLU cc_start: 0.8674 (mp0) cc_final: 0.8333 (pt0) REVERT: C 81 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9152 (mp) REVERT: C 268 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8093 (mp) REVERT: C 372 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8609 (mt-10) REVERT: C 375 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7588 (pt) outliers start: 21 outliers final: 10 residues processed: 159 average time/residue: 0.4102 time to fit residues: 70.8486 Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.0000 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086881 restraints weight = 18093.928| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.16 r_work: 0.2997 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8580 Z= 0.135 Angle : 0.572 6.671 11670 Z= 0.281 Chirality : 0.040 0.136 1344 Planarity : 0.004 0.046 1395 Dihedral : 11.211 117.205 1322 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.69 % Allowed : 22.15 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.26), residues: 1059 helix: 2.25 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.35 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 374 TYR 0.012 0.001 TYR A 369 PHE 0.008 0.001 PHE A 288 TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8580) covalent geometry : angle 0.57240 (11670) hydrogen bonds : bond 0.04331 ( 551) hydrogen bonds : angle 3.55774 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8080 (m) REVERT: B 39 THR cc_start: 0.8021 (t) cc_final: 0.7712 (m) REVERT: B 279 GLU cc_start: 0.8675 (mp0) cc_final: 0.8306 (pt0) REVERT: C 81 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9161 (mp) REVERT: C 201 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8707 (mttm) REVERT: C 372 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8598 (mt-10) outliers start: 32 outliers final: 12 residues processed: 163 average time/residue: 0.4149 time to fit residues: 73.2004 Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.085183 restraints weight = 18091.959| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.12 r_work: 0.2983 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8580 Z= 0.163 Angle : 0.596 6.657 11670 Z= 0.292 Chirality : 0.041 0.138 1344 Planarity : 0.004 0.046 1395 Dihedral : 11.252 113.338 1322 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.77 % Allowed : 23.30 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.26), residues: 1059 helix: 2.22 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.33 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.013 0.001 TYR A 369 PHE 0.008 0.001 PHE A 288 TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8580) covalent geometry : angle 0.59556 (11670) hydrogen bonds : bond 0.04617 ( 551) hydrogen bonds : angle 3.64051 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8444 (mt-10) REVERT: B 39 THR cc_start: 0.8037 (t) cc_final: 0.7683 (m) REVERT: B 279 GLU cc_start: 0.8678 (mp0) cc_final: 0.8330 (pt0) REVERT: C 81 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9219 (mp) REVERT: C 237 ASP cc_start: 0.8862 (p0) cc_final: 0.8656 (p0) REVERT: C 372 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8608 (mt-10) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.4570 time to fit residues: 73.6660 Evaluate side-chains 148 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086978 restraints weight = 18093.867| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.18 r_work: 0.2997 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8580 Z= 0.125 Angle : 0.580 8.035 11670 Z= 0.286 Chirality : 0.039 0.137 1344 Planarity : 0.004 0.046 1395 Dihedral : 11.153 112.366 1322 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.42 % Allowed : 23.18 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.26), residues: 1059 helix: 2.24 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.29 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 114 TYR 0.012 0.001 TYR B 369 PHE 0.007 0.001 PHE B 160 TRP 0.012 0.001 TRP A 340 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8580) covalent geometry : angle 0.58005 (11670) hydrogen bonds : bond 0.04277 ( 551) hydrogen bonds : angle 3.55313 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.8266 (mtp) cc_final: 0.7985 (mtm) REVERT: A 372 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8468 (mt-10) REVERT: B 39 THR cc_start: 0.8121 (t) cc_final: 0.7795 (m) REVERT: B 279 GLU cc_start: 0.8704 (mp0) cc_final: 0.8355 (pt0) REVERT: C 81 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9160 (mp) REVERT: C 372 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8603 (mt-10) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.4391 time to fit residues: 70.7796 Evaluate side-chains 146 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088057 restraints weight = 17885.093| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.17 r_work: 0.3029 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8580 Z= 0.120 Angle : 0.594 7.968 11670 Z= 0.290 Chirality : 0.039 0.137 1344 Planarity : 0.004 0.044 1395 Dihedral : 11.053 108.206 1322 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 24.11 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.26), residues: 1059 helix: 2.23 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.29 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 114 TYR 0.013 0.001 TYR B 369 PHE 0.011 0.001 PHE B 160 TRP 0.011 0.001 TRP A 340 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8580) covalent geometry : angle 0.59363 (11670) hydrogen bonds : bond 0.04166 ( 551) hydrogen bonds : angle 3.55206 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 39 THR cc_start: 0.8083 (t) cc_final: 0.7765 (m) REVERT: B 279 GLU cc_start: 0.8684 (mp0) cc_final: 0.8342 (pt0) REVERT: B 300 MET cc_start: 0.8762 (tpt) cc_final: 0.8519 (tpp) REVERT: C 81 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9159 (mp) REVERT: C 204 ILE cc_start: 0.9179 (tt) cc_final: 0.8932 (pp) REVERT: C 372 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8580 (mt-10) outliers start: 15 outliers final: 10 residues processed: 146 average time/residue: 0.4367 time to fit residues: 69.0214 Evaluate side-chains 147 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 379 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 6 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.088254 restraints weight = 17875.622| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.17 r_work: 0.3020 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8580 Z= 0.121 Angle : 0.588 7.898 11670 Z= 0.289 Chirality : 0.039 0.136 1344 Planarity : 0.004 0.044 1395 Dihedral : 10.972 104.257 1322 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.65 % Allowed : 22.84 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.26), residues: 1059 helix: 2.22 (0.18), residues: 783 sheet: None (None), residues: 0 loop : 1.29 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 374 TYR 0.014 0.001 TYR B 369 PHE 0.007 0.001 PHE B 160 TRP 0.010 0.001 TRP A 340 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8580) covalent geometry : angle 0.58798 (11670) hydrogen bonds : bond 0.04163 ( 551) hydrogen bonds : angle 3.52543 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.56 seconds wall clock time: 45 minutes 37.65 seconds (2737.65 seconds total)