Starting phenix.real_space_refine on Wed Sep 17 21:24:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.map" model { file = "/net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k10_8192/09_2025/5k10_8192.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6334 atoms to isotropic. 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 38 5.16 5 C 4016 2.51 5 N 1074 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.48, per 1000 atoms: 0.39 Number of scatterers: 6338 At special positions: 0 Unit cell: (99.495, 76.725, 82.665, 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 38 16.00 P 6 15.00 O 1204 8.00 N 1074 7.00 C 4016 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 422.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 46.6% alpha, 13.6% 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 16 through 31 removed outlier: 4.085A pdb=" N ILE A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.807A pdb=" N LYS A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.754A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.922A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 204 Processing helix chain 'A' and resid 216 through 234 removed outlier: 3.625A pdb=" N ASP A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.414A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.574A pdb=" N TRP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 369 removed outlier: 3.573A pdb=" N ALA A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.769A pdb=" N LYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.889A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 401 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 removed outlier: 4.086A pdb=" N ILE B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.808A pdb=" N LYS B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.754A pdb=" N GLU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.922A pdb=" N ILE B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 204 Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.625A pdb=" N ASP B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.414A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.574A pdb=" N TRP B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 369 removed outlier: 3.573A pdb=" N ALA B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 381 removed outlier: 3.768A pdb=" N LYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.888A pdb=" N LYS B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 401 " --> pdb=" O PHE B 397 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 4.272A pdb=" N SER A 6 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP A 38 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A 8 " --> pdb=" O ASP A 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.782A pdb=" N ALA A 307 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL A 107 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 132 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE A 129 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYS A 269 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY A 131 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG A 249 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 209 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 9 removed outlier: 4.272A pdb=" N SER B 6 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP B 38 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY B 8 " --> pdb=" O ASP B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.781A pdb=" N ALA B 307 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL B 107 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 132 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 129 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYS B 269 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 131 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG B 249 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 209 " --> pdb=" O ARG B 249 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 816 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: 1.04 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2032 1.34 - 1.46: 1468 1.46 - 1.58: 2896 1.58 - 1.70: 6 1.70 - 1.82: 68 Bond restraints: 6470 Sorted by residual: bond pdb=" CB PHE B 334 " pdb=" CG PHE B 334 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 3.03e+00 bond pdb=" CB PHE A 334 " pdb=" CG PHE A 334 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 2.98e+00 bond pdb=" CB TRP A 267 " pdb=" CG TRP A 267 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.96e+00 bond pdb=" CB TRP B 267 " pdb=" CG TRP B 267 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.91e+00 bond pdb=" CE3 TRP A 267 " pdb=" CZ3 TRP A 267 " ideal model delta sigma weight residual 1.382 1.334 0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 6465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 8257 1.84 - 3.69: 414 3.69 - 5.53: 49 5.53 - 7.38: 14 7.38 - 9.22: 2 Bond angle restraints: 8736 Sorted by residual: angle pdb=" N ARG A 314 " pdb=" CA ARG A 314 " pdb=" C ARG A 314 " ideal model delta sigma weight residual 110.53 104.79 5.74 1.32e+00 5.74e-01 1.89e+01 angle pdb=" N ARG B 314 " pdb=" CA ARG B 314 " pdb=" C ARG B 314 " ideal model delta sigma weight residual 110.53 104.81 5.72 1.32e+00 5.74e-01 1.87e+01 angle pdb=" N VAL B 296 " pdb=" CA VAL B 296 " pdb=" C VAL B 296 " ideal model delta sigma weight residual 108.86 114.58 -5.72 1.63e+00 3.76e-01 1.23e+01 angle pdb=" N VAL A 296 " pdb=" CA VAL A 296 " pdb=" C VAL A 296 " ideal model delta sigma weight residual 108.86 114.54 -5.68 1.63e+00 3.76e-01 1.21e+01 angle pdb=" CA THR B 313 " pdb=" C THR B 313 " pdb=" N ARG B 314 " ideal model delta sigma weight residual 117.30 113.64 3.66 1.16e+00 7.43e-01 9.97e+00 ... (remaining 8731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 3750 24.77 - 49.55: 70 49.55 - 74.32: 14 74.32 - 99.09: 6 99.09 - 123.87: 2 Dihedral angle restraints: 3842 sinusoidal: 1564 harmonic: 2278 Sorted by residual: dihedral pdb=" CD ARG A 314 " pdb=" NE ARG A 314 " pdb=" CZ ARG A 314 " pdb=" NH1 ARG A 314 " ideal model delta sinusoidal sigma weight residual 0.00 -62.90 62.90 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CD ARG B 314 " pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH1 ARG B 314 " ideal model delta sinusoidal sigma weight residual 0.00 -62.88 62.88 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA GLN A 242 " pdb=" C GLN A 242 " pdb=" N LYS A 243 " pdb=" CA LYS A 243 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 3839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 634 0.053 - 0.105: 263 0.105 - 0.158: 49 0.158 - 0.211: 6 0.211 - 0.263: 2 Chirality restraints: 954 Sorted by residual: chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE B 244 " pdb=" CA ILE B 244 " pdb=" CG1 ILE B 244 " pdb=" CG2 ILE B 244 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A 5 " pdb=" CA ILE A 5 " pdb=" CG1 ILE A 5 " pdb=" CG2 ILE A 5 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 951 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 314 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.17e+02 pdb=" NE ARG A 314 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 314 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 314 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 314 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.16e+02 pdb=" NE ARG B 314 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 227 " -0.017 2.00e-02 2.50e+03 2.36e-02 9.73e+00 pdb=" CG PHE B 227 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 227 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 227 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 227 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 227 " -0.005 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 269 2.69 - 3.24: 7059 3.24 - 3.80: 10501 3.80 - 4.35: 14213 4.35 - 4.90: 22358 Nonbonded interactions: 54400 Sorted by model distance: nonbonded pdb=" O GLY A 148 " pdb=" OH TYR B 156 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" O GLY B 148 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP B 347 " pdb=" ND2 ASN B 349 " model vdw 2.174 3.120 nonbonded pdb=" OD2 ASP A 347 " pdb=" ND2 ASN A 349 " model vdw 2.175 3.120 nonbonded pdb=" OE2 GLU B 12 " pdb=" NE1 TRP B 23 " model vdw 2.187 3.120 ... (remaining 54395 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 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 : 0.015 0.716 6472 Z= 1.315 Angle : 0.928 9.219 8736 Z= 0.515 Chirality : 0.056 0.263 954 Planarity : 0.020 0.439 1104 Dihedral : 12.219 123.867 2378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 33.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.91 % Favored : 92.58 % Rotamer: Outliers : 0.30 % Allowed : 2.42 % Favored : 97.28 % 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 aren not related in a simple way. whole: -4.07 (0.25), residues: 782 helix: -3.57 (0.22), residues: 242 sheet: -2.83 (0.29), residues: 174 loop : -1.80 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 49 TYR 0.036 0.004 TYR A 156 PHE 0.051 0.004 PHE B 227 TRP 0.025 0.004 TRP A 267 HIS 0.008 0.002 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00859 ( 6470) covalent geometry : angle 0.92779 ( 8736) hydrogen bonds : bond 0.31097 ( 286) hydrogen bonds : angle 10.46486 ( 816) Misc. bond : bond 0.71547 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 186 average time/residue: 0.1477 time to fit residues: 32.6216 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 228 GLN A 349 ASN A 385 ASN B 96 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 349 ASN B 385 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.043364 restraints weight = 36306.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044883 restraints weight = 24994.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045998 restraints weight = 18820.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.046851 restraints weight = 15145.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.047546 restraints weight = 12772.950| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6472 Z= 0.200 Angle : 0.758 7.239 8736 Z= 0.402 Chirality : 0.047 0.157 954 Planarity : 0.005 0.052 1104 Dihedral : 9.870 120.409 868 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.42 % Rotamer: Outliers : 3.02 % Allowed : 11.63 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.26), residues: 782 helix: -1.11 (0.26), residues: 328 sheet: -1.93 (0.34), residues: 162 loop : -1.56 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 109 TYR 0.013 0.001 TYR B 235 PHE 0.021 0.002 PHE A 197 TRP 0.031 0.003 TRP B 124 HIS 0.009 0.002 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6470) covalent geometry : angle 0.75753 ( 8736) hydrogen bonds : bond 0.05206 ( 286) hydrogen bonds : angle 6.24314 ( 816) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9292 (mm) REVERT: A 180 MET cc_start: 0.8225 (ppp) cc_final: 0.5081 (tmm) REVERT: A 182 MET cc_start: 0.8126 (tpp) cc_final: 0.7877 (mtp) REVERT: A 223 PHE cc_start: 0.9144 (m-80) cc_final: 0.8741 (m-80) REVERT: A 227 PHE cc_start: 0.9569 (m-80) cc_final: 0.9291 (m-10) REVERT: B 44 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9314 (mm) REVERT: B 91 MET cc_start: 0.9097 (mmt) cc_final: 0.8896 (mmm) REVERT: B 153 GLU cc_start: 0.8592 (pt0) cc_final: 0.8342 (pm20) REVERT: B 182 MET cc_start: 0.8095 (ttp) cc_final: 0.6293 (mtp) REVERT: B 223 PHE cc_start: 0.9164 (m-80) cc_final: 0.8774 (m-80) REVERT: B 227 PHE cc_start: 0.9564 (m-80) cc_final: 0.9304 (m-80) REVERT: B 291 MET cc_start: 0.9367 (mpp) cc_final: 0.9138 (mmm) outliers start: 20 outliers final: 8 residues processed: 118 average time/residue: 0.0859 time to fit residues: 13.5343 Evaluate side-chains 82 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.041811 restraints weight = 34917.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043271 restraints weight = 23588.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044358 restraints weight = 17628.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045266 restraints weight = 14216.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045961 restraints weight = 11809.158| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6472 Z= 0.174 Angle : 0.681 5.590 8736 Z= 0.357 Chirality : 0.043 0.145 954 Planarity : 0.004 0.038 1104 Dihedral : 9.622 118.765 868 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.09 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 15.56 % Favored : 82.48 % 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 aren not related in a simple way. whole: -1.19 (0.29), residues: 782 helix: 0.02 (0.29), residues: 314 sheet: -1.27 (0.37), residues: 156 loop : -1.21 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 TYR 0.016 0.001 TYR B 231 PHE 0.018 0.002 PHE A 197 TRP 0.014 0.002 TRP B 124 HIS 0.006 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6470) covalent geometry : angle 0.68118 ( 8736) hydrogen bonds : bond 0.04102 ( 286) hydrogen bonds : angle 5.73331 ( 816) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.9357 (mmm) cc_final: 0.9126 (mmm) REVERT: A 44 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9222 (mm) REVERT: A 180 MET cc_start: 0.8287 (ppp) cc_final: 0.5473 (tmm) REVERT: A 223 PHE cc_start: 0.9181 (m-80) cc_final: 0.8701 (m-80) REVERT: A 227 PHE cc_start: 0.9513 (m-80) cc_final: 0.9278 (m-80) REVERT: A 254 MET cc_start: 0.9070 (tpp) cc_final: 0.8806 (tpp) REVERT: A 290 MET cc_start: 0.8959 (mmp) cc_final: 0.8736 (mtt) REVERT: A 291 MET cc_start: 0.9412 (mmm) cc_final: 0.9114 (mmm) REVERT: A 360 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9087 (mp0) REVERT: B 18 MET cc_start: 0.9360 (mmm) cc_final: 0.9135 (mmm) REVERT: B 44 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9248 (mm) REVERT: B 182 MET cc_start: 0.8148 (ttp) cc_final: 0.6470 (mtp) REVERT: B 223 PHE cc_start: 0.9185 (m-80) cc_final: 0.8711 (m-80) REVERT: B 227 PHE cc_start: 0.9516 (m-80) cc_final: 0.9274 (m-80) REVERT: B 254 MET cc_start: 0.9056 (tpp) cc_final: 0.8795 (tpp) REVERT: B 291 MET cc_start: 0.9412 (mpp) cc_final: 0.9155 (mmm) REVERT: B 360 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9119 (mp0) REVERT: B 372 MET cc_start: 0.8543 (ptp) cc_final: 0.7223 (mtt) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.0870 time to fit residues: 10.9897 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 40.0000 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.042000 restraints weight = 34324.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.043493 restraints weight = 23049.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044618 restraints weight = 17136.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045452 restraints weight = 13657.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046198 restraints weight = 11335.325| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6472 Z= 0.135 Angle : 0.596 5.026 8736 Z= 0.311 Chirality : 0.042 0.124 954 Planarity : 0.003 0.031 1104 Dihedral : 9.336 116.460 868 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.78 % Rotamer: Outliers : 3.47 % Allowed : 13.90 % Favored : 82.63 % 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 aren not related in a simple way. whole: -0.81 (0.29), residues: 782 helix: 0.18 (0.29), residues: 330 sheet: -0.94 (0.37), residues: 168 loop : -0.94 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 109 TYR 0.013 0.001 TYR A 231 PHE 0.013 0.002 PHE A 197 TRP 0.014 0.002 TRP B 245 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6470) covalent geometry : angle 0.59555 ( 8736) hydrogen bonds : bond 0.03530 ( 286) hydrogen bonds : angle 5.44291 ( 816) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9191 (mmp) cc_final: 0.8652 (mpp) REVERT: A 180 MET cc_start: 0.8565 (ppp) cc_final: 0.8049 (tmm) REVERT: A 223 PHE cc_start: 0.9171 (m-80) cc_final: 0.8617 (m-80) REVERT: A 227 PHE cc_start: 0.9492 (m-80) cc_final: 0.9251 (m-80) REVERT: A 254 MET cc_start: 0.9058 (tpp) cc_final: 0.8569 (tpp) REVERT: A 267 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8916 (t-100) REVERT: A 291 MET cc_start: 0.9388 (mmm) cc_final: 0.9126 (mmm) REVERT: B 84 GLU cc_start: 0.9329 (pt0) cc_final: 0.9018 (pp20) REVERT: B 180 MET cc_start: 0.8599 (ppp) cc_final: 0.8076 (ppp) REVERT: B 223 PHE cc_start: 0.9170 (m-80) cc_final: 0.8624 (m-80) REVERT: B 227 PHE cc_start: 0.9496 (m-80) cc_final: 0.9258 (m-80) REVERT: B 254 MET cc_start: 0.9048 (tpp) cc_final: 0.8526 (tpp) REVERT: B 267 TRP cc_start: 0.9241 (OUTLIER) cc_final: 0.8906 (t-100) REVERT: B 291 MET cc_start: 0.9379 (mpp) cc_final: 0.9117 (mmm) outliers start: 23 outliers final: 11 residues processed: 99 average time/residue: 0.1047 time to fit residues: 13.1951 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 7 optimal weight: 0.0040 chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 53 optimal weight: 30.0000 overall best weight: 6.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.054087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041507 restraints weight = 36545.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.042977 restraints weight = 24576.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044079 restraints weight = 18292.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.044986 restraints weight = 14565.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045616 restraints weight = 12070.866| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6472 Z= 0.160 Angle : 0.636 5.568 8736 Z= 0.329 Chirality : 0.042 0.125 954 Planarity : 0.003 0.027 1104 Dihedral : 9.234 117.317 868 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.71 % Favored : 96.04 % Rotamer: Outliers : 2.72 % Allowed : 15.56 % Favored : 81.72 % 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 aren not related in a simple way. whole: -0.50 (0.30), residues: 782 helix: 0.46 (0.29), residues: 326 sheet: -0.93 (0.38), residues: 166 loop : -0.68 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 109 TYR 0.013 0.001 TYR B 231 PHE 0.011 0.002 PHE A 334 TRP 0.011 0.002 TRP B 267 HIS 0.005 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6470) covalent geometry : angle 0.63560 ( 8736) hydrogen bonds : bond 0.03399 ( 286) hydrogen bonds : angle 5.47227 ( 816) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9163 (mmp) cc_final: 0.8739 (mpp) REVERT: A 84 GLU cc_start: 0.9355 (pt0) cc_final: 0.9049 (pp20) REVERT: A 180 MET cc_start: 0.8518 (ppp) cc_final: 0.7892 (tmm) REVERT: A 223 PHE cc_start: 0.9171 (m-80) cc_final: 0.8620 (m-80) REVERT: A 254 MET cc_start: 0.9075 (tpp) cc_final: 0.8739 (mpp) REVERT: A 291 MET cc_start: 0.9411 (mmm) cc_final: 0.9062 (mmm) REVERT: B 84 GLU cc_start: 0.9350 (pt0) cc_final: 0.9039 (pp20) REVERT: B 180 MET cc_start: 0.8541 (ppp) cc_final: 0.8036 (ppp) REVERT: B 182 MET cc_start: 0.8159 (tpt) cc_final: 0.7838 (tmm) REVERT: B 223 PHE cc_start: 0.9164 (m-80) cc_final: 0.8564 (m-80) REVERT: B 227 PHE cc_start: 0.9526 (m-80) cc_final: 0.9312 (m-80) REVERT: B 254 MET cc_start: 0.9083 (tpp) cc_final: 0.8832 (tpp) REVERT: B 291 MET cc_start: 0.9380 (mpp) cc_final: 0.9156 (mmm) outliers start: 18 outliers final: 13 residues processed: 87 average time/residue: 0.0878 time to fit residues: 10.2431 Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.053114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040828 restraints weight = 34985.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.042203 restraints weight = 23380.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043317 restraints weight = 17518.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044166 restraints weight = 13824.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044750 restraints weight = 11427.721| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6472 Z= 0.151 Angle : 0.622 6.539 8736 Z= 0.324 Chirality : 0.042 0.125 954 Planarity : 0.003 0.025 1104 Dihedral : 9.145 116.372 868 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.78 % Rotamer: Outliers : 2.57 % Allowed : 15.41 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -0.40 (0.30), residues: 782 helix: 0.65 (0.29), residues: 328 sheet: -0.89 (0.37), residues: 164 loop : -0.80 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 109 TYR 0.012 0.001 TYR B 231 PHE 0.014 0.002 PHE A 371 TRP 0.011 0.001 TRP B 267 HIS 0.009 0.002 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6470) covalent geometry : angle 0.62233 ( 8736) hydrogen bonds : bond 0.03191 ( 286) hydrogen bonds : angle 5.46161 ( 816) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9152 (mmt) cc_final: 0.8787 (mpp) REVERT: A 84 GLU cc_start: 0.9309 (pt0) cc_final: 0.9032 (pp20) REVERT: A 91 MET cc_start: 0.8955 (tpp) cc_final: 0.8695 (tpp) REVERT: A 180 MET cc_start: 0.8529 (ppp) cc_final: 0.7901 (tmm) REVERT: A 223 PHE cc_start: 0.9184 (m-80) cc_final: 0.8594 (m-80) REVERT: A 254 MET cc_start: 0.9017 (tpp) cc_final: 0.8554 (mpp) REVERT: A 267 TRP cc_start: 0.9258 (OUTLIER) cc_final: 0.8970 (t-100) REVERT: A 291 MET cc_start: 0.9393 (mmm) cc_final: 0.9045 (mmm) REVERT: B 84 GLU cc_start: 0.9313 (pt0) cc_final: 0.9009 (pp20) REVERT: B 180 MET cc_start: 0.8499 (ppp) cc_final: 0.8002 (ppp) REVERT: B 182 MET cc_start: 0.8013 (tpt) cc_final: 0.7706 (tmm) REVERT: B 223 PHE cc_start: 0.9166 (m-80) cc_final: 0.8574 (m-80) REVERT: B 254 MET cc_start: 0.9030 (tpp) cc_final: 0.8535 (mpp) REVERT: B 267 TRP cc_start: 0.9251 (OUTLIER) cc_final: 0.8913 (t-100) REVERT: B 291 MET cc_start: 0.9357 (mpp) cc_final: 0.8981 (mmm) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.0852 time to fit residues: 9.6454 Evaluate side-chains 73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 10.0000 chunk 34 optimal weight: 40.0000 chunk 74 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040053 restraints weight = 36837.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041451 restraints weight = 24872.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.042567 restraints weight = 18516.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.043420 restraints weight = 14667.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.043873 restraints weight = 12171.194| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6472 Z= 0.196 Angle : 0.655 7.943 8736 Z= 0.342 Chirality : 0.042 0.131 954 Planarity : 0.004 0.026 1104 Dihedral : 9.079 115.669 868 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 3.17 % Allowed : 16.01 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -0.53 (0.30), residues: 782 helix: 0.57 (0.29), residues: 334 sheet: -1.07 (0.36), residues: 168 loop : -0.84 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 317 TYR 0.013 0.002 TYR B 231 PHE 0.010 0.002 PHE A 334 TRP 0.011 0.002 TRP B 267 HIS 0.007 0.002 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6470) covalent geometry : angle 0.65532 ( 8736) hydrogen bonds : bond 0.03515 ( 286) hydrogen bonds : angle 5.45791 ( 816) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9205 (mmt) cc_final: 0.8764 (mpp) REVERT: A 84 GLU cc_start: 0.9354 (pt0) cc_final: 0.9086 (pp20) REVERT: A 91 MET cc_start: 0.9107 (tpp) cc_final: 0.8904 (mmm) REVERT: A 180 MET cc_start: 0.8535 (ppp) cc_final: 0.7955 (tmm) REVERT: A 223 PHE cc_start: 0.9216 (m-80) cc_final: 0.8613 (m-80) REVERT: A 254 MET cc_start: 0.9066 (tpp) cc_final: 0.8609 (mpp) REVERT: A 267 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8979 (t-100) REVERT: A 291 MET cc_start: 0.9418 (mmm) cc_final: 0.9066 (mmm) REVERT: A 334 PHE cc_start: 0.9720 (m-80) cc_final: 0.9355 (m-80) REVERT: B 84 GLU cc_start: 0.9343 (pt0) cc_final: 0.9051 (pp20) REVERT: B 180 MET cc_start: 0.8473 (ppp) cc_final: 0.8124 (ppp) REVERT: B 182 MET cc_start: 0.7964 (tpt) cc_final: 0.7703 (tmm) REVERT: B 223 PHE cc_start: 0.9199 (m-80) cc_final: 0.8590 (m-80) REVERT: B 254 MET cc_start: 0.9027 (tpp) cc_final: 0.8613 (mpp) REVERT: B 267 TRP cc_start: 0.9261 (OUTLIER) cc_final: 0.8974 (t-100) REVERT: B 291 MET cc_start: 0.9370 (mpp) cc_final: 0.9067 (mmm) REVERT: B 398 MET cc_start: 0.9511 (mmp) cc_final: 0.9297 (mpp) outliers start: 21 outliers final: 13 residues processed: 80 average time/residue: 0.0737 time to fit residues: 8.2128 Evaluate side-chains 75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040536 restraints weight = 36122.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.041974 restraints weight = 24060.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.043098 restraints weight = 17787.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.043879 restraints weight = 13984.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044585 restraints weight = 11662.307| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6472 Z= 0.142 Angle : 0.656 8.193 8736 Z= 0.340 Chirality : 0.043 0.126 954 Planarity : 0.003 0.026 1104 Dihedral : 8.843 109.824 868 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.58 % Favored : 96.16 % Rotamer: Outliers : 2.27 % Allowed : 17.82 % Favored : 79.91 % 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 aren not related in a simple way. whole: -0.31 (0.30), residues: 782 helix: 0.79 (0.29), residues: 330 sheet: -0.82 (0.38), residues: 150 loop : -0.86 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.011 0.001 TYR B 231 PHE 0.010 0.001 PHE B 371 TRP 0.011 0.001 TRP B 267 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6470) covalent geometry : angle 0.65626 ( 8736) hydrogen bonds : bond 0.03416 ( 286) hydrogen bonds : angle 5.34946 ( 816) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9166 (mmt) cc_final: 0.8800 (mpp) REVERT: A 84 GLU cc_start: 0.9329 (pt0) cc_final: 0.9096 (pp20) REVERT: A 180 MET cc_start: 0.8486 (ppp) cc_final: 0.7894 (tmm) REVERT: A 223 PHE cc_start: 0.9199 (m-80) cc_final: 0.8563 (m-80) REVERT: A 254 MET cc_start: 0.8996 (tpp) cc_final: 0.8758 (mpp) REVERT: A 291 MET cc_start: 0.9402 (mmm) cc_final: 0.9035 (mmm) REVERT: B 180 MET cc_start: 0.8462 (ppp) cc_final: 0.8102 (ppp) REVERT: B 182 MET cc_start: 0.7924 (tpt) cc_final: 0.7675 (tmm) REVERT: B 223 PHE cc_start: 0.9185 (m-80) cc_final: 0.8530 (m-80) REVERT: B 290 MET cc_start: 0.8968 (mmp) cc_final: 0.8587 (mtt) REVERT: B 291 MET cc_start: 0.9362 (mpp) cc_final: 0.8859 (mmm) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.0741 time to fit residues: 8.0492 Evaluate side-chains 73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 40.0000 chunk 66 optimal weight: 50.0000 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040313 restraints weight = 35925.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041706 restraints weight = 24086.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.042779 restraints weight = 17830.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.043639 restraints weight = 14063.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044283 restraints weight = 11601.215| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6472 Z= 0.145 Angle : 0.667 9.641 8736 Z= 0.343 Chirality : 0.043 0.136 954 Planarity : 0.003 0.027 1104 Dihedral : 8.614 104.744 868 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 1.81 % Allowed : 18.58 % Favored : 79.61 % 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 aren not related in a simple way. whole: -0.26 (0.30), residues: 782 helix: 0.74 (0.29), residues: 330 sheet: -0.74 (0.38), residues: 150 loop : -0.76 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.013 0.001 TYR B 316 PHE 0.008 0.001 PHE A 371 TRP 0.011 0.001 TRP A 267 HIS 0.004 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6470) covalent geometry : angle 0.66660 ( 8736) hydrogen bonds : bond 0.03457 ( 286) hydrogen bonds : angle 5.25932 ( 816) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9171 (mmt) cc_final: 0.8792 (mpp) REVERT: A 84 GLU cc_start: 0.9310 (pt0) cc_final: 0.9079 (pp20) REVERT: A 91 MET cc_start: 0.8840 (tpp) cc_final: 0.8518 (tpp) REVERT: A 180 MET cc_start: 0.8463 (ppp) cc_final: 0.7882 (tmm) REVERT: A 223 PHE cc_start: 0.9196 (m-80) cc_final: 0.8541 (m-80) REVERT: A 254 MET cc_start: 0.8958 (tpp) cc_final: 0.8520 (mpp) REVERT: A 267 TRP cc_start: 0.9264 (OUTLIER) cc_final: 0.8878 (t-100) REVERT: A 291 MET cc_start: 0.9402 (mmm) cc_final: 0.9047 (mmm) REVERT: B 180 MET cc_start: 0.8439 (ppp) cc_final: 0.8065 (ppp) REVERT: B 182 MET cc_start: 0.7875 (tpt) cc_final: 0.7642 (tmm) REVERT: B 223 PHE cc_start: 0.9203 (m-80) cc_final: 0.8540 (m-80) REVERT: B 254 MET cc_start: 0.8859 (tpp) cc_final: 0.8500 (mpp) REVERT: B 267 TRP cc_start: 0.9305 (OUTLIER) cc_final: 0.8883 (t-100) REVERT: B 291 MET cc_start: 0.9357 (mpp) cc_final: 0.8986 (mmm) REVERT: B 398 MET cc_start: 0.9489 (mmp) cc_final: 0.8994 (mtt) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0694 time to fit residues: 7.4103 Evaluate side-chains 75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 40.0000 chunk 59 optimal weight: 0.0270 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 34 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.052224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.040122 restraints weight = 36096.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.041509 restraints weight = 24156.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.042626 restraints weight = 17923.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.043460 restraints weight = 14056.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.044098 restraints weight = 11609.810| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6472 Z= 0.152 Angle : 0.668 9.606 8736 Z= 0.343 Chirality : 0.043 0.125 954 Planarity : 0.003 0.026 1104 Dihedral : 8.570 104.601 868 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.27 % Rotamer: Outliers : 1.51 % Allowed : 19.34 % Favored : 79.15 % 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 aren not related in a simple way. whole: -0.23 (0.30), residues: 782 helix: 0.77 (0.29), residues: 330 sheet: -0.75 (0.39), residues: 150 loop : -0.73 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.011 0.001 TYR B 231 PHE 0.009 0.001 PHE B 371 TRP 0.011 0.001 TRP A 267 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6470) covalent geometry : angle 0.66766 ( 8736) hydrogen bonds : bond 0.03393 ( 286) hydrogen bonds : angle 5.23760 ( 816) Misc. bond : bond 0.00020 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.9173 (mmt) cc_final: 0.8796 (mpp) REVERT: A 84 GLU cc_start: 0.9320 (pt0) cc_final: 0.9102 (pp20) REVERT: A 91 MET cc_start: 0.8895 (tpp) cc_final: 0.8542 (tpp) REVERT: A 180 MET cc_start: 0.8445 (ppp) cc_final: 0.7877 (tmm) REVERT: A 223 PHE cc_start: 0.9204 (m-80) cc_final: 0.8528 (m-80) REVERT: A 254 MET cc_start: 0.8942 (tpp) cc_final: 0.8528 (mpp) REVERT: A 267 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8907 (t-100) REVERT: A 291 MET cc_start: 0.9404 (mmm) cc_final: 0.9044 (mmm) REVERT: B 180 MET cc_start: 0.8381 (ppp) cc_final: 0.8033 (ppp) REVERT: B 198 GLN cc_start: 0.9737 (mm-40) cc_final: 0.9271 (mm110) REVERT: B 223 PHE cc_start: 0.9211 (m-80) cc_final: 0.8550 (m-80) REVERT: B 291 MET cc_start: 0.9356 (mpp) cc_final: 0.9000 (mmm) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.0690 time to fit residues: 7.4567 Evaluate side-chains 72 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 40.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.053519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.041780 restraints weight = 37468.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.043243 restraints weight = 24634.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044391 restraints weight = 18027.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045223 restraints weight = 14103.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045870 restraints weight = 11584.118| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6472 Z= 0.145 Angle : 0.691 10.181 8736 Z= 0.354 Chirality : 0.043 0.144 954 Planarity : 0.003 0.024 1104 Dihedral : 8.570 104.330 868 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 1.66 % Allowed : 19.94 % Favored : 78.40 % 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 aren not related in a simple way. whole: -0.24 (0.30), residues: 782 helix: 0.74 (0.29), residues: 330 sheet: -0.64 (0.39), residues: 148 loop : -0.78 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.012 0.001 TYR B 219 PHE 0.009 0.001 PHE A 371 TRP 0.012 0.001 TRP B 267 HIS 0.004 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6470) covalent geometry : angle 0.69081 ( 8736) hydrogen bonds : bond 0.03415 ( 286) hydrogen bonds : angle 5.26715 ( 816) Misc. bond : bond 0.00024 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1223.44 seconds wall clock time: 21 minutes 57.18 seconds (1317.18 seconds total)