Starting phenix.real_space_refine on Tue Feb 3 16:01:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kgi_62320/02_2026/9kgi_62320.map" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2971 2.51 5 N 762 2.21 5 O 933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4686 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2306 Classifications: {'peptide': 303} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 26, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2314 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 26, 'TRANS': 276} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'FUC': 1, 'GLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'FUC': 1, 'GLA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.82, per 1000 atoms: 0.17 Number of scatterers: 4686 At special positions: 0 Unit cell: (76.7, 70.85, 76.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 933 8.00 N 762 7.00 C 2971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " GLA C 1 " - " GLA C 3 " " GLA D 1 " - " GLA D 3 " BETA1-2 " GLA C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " GLA D 1 " - " FUC D 2 " Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 186.7 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1086 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 10 sheets defined 7.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.608A pdb=" N LEU A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.781A pdb=" N ILE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 353 through 357 removed outlier: 4.116A pdb=" N ASP B 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.608A pdb=" N LEU B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.982A pdb=" N ILE B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA2, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA3, first strand: chain 'B' and resid 427 through 429 removed outlier: 4.397A pdb=" N MET A 345 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP A 285 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY A 277 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 287 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 15.821A pdb=" N ARG A 377 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 13.379A pdb=" N PHE A 327 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 379 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE A 381 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 15.063A pdb=" N GLU A 331 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 324 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET A 345 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS A 326 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA A 343 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR A 328 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 341 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 386 removed outlier: 4.367A pdb=" N ALA A 385 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 429 removed outlier: 5.810A pdb=" N ALA A 427 " --> pdb=" O TYR B 338 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP B 340 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N SER A 429 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP B 342 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL B 341 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR B 328 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS B 326 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET B 345 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 324 " --> pdb=" O MET B 345 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N HIS B 323 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA B 385 " --> pdb=" O HIS B 323 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL B 325 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET B 383 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 327 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 329 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG B 377 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA B 385 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 429 removed outlier: 5.810A pdb=" N ALA A 427 " --> pdb=" O TYR B 338 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP B 340 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N SER A 429 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP B 342 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET B 345 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP B 285 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY B 277 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 287 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA B 385 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 490 removed outlier: 4.295A pdb=" N VAL A 477 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA A 465 " --> pdb=" O TRP A 513 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP A 513 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 467 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 490 removed outlier: 6.502A pdb=" N ALA B 465 " --> pdb=" O TRP B 513 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TRP B 513 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 467 " --> pdb=" O ASN B 511 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 910 1.33 - 1.45: 1305 1.45 - 1.57: 2586 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 4833 Sorted by residual: bond pdb=" CA ALA A 288 " pdb=" CB ALA A 288 " ideal model delta sigma weight residual 1.535 1.479 0.056 1.32e-02 5.74e+03 1.77e+01 bond pdb=" N VAL B 439 " pdb=" CA VAL B 439 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" N VAL A 439 " pdb=" CA VAL A 439 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.64e+00 bond pdb=" N VAL A 316 " pdb=" CA VAL A 316 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.15e+00 bond pdb=" N VAL A 436 " pdb=" CA VAL A 436 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.18e-02 7.18e+03 7.83e+00 ... (remaining 4828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 6185 1.34 - 2.68: 327 2.68 - 4.02: 85 4.02 - 5.36: 22 5.36 - 6.70: 6 Bond angle restraints: 6625 Sorted by residual: angle pdb=" C HIS A 323 " pdb=" CA HIS A 323 " pdb=" CB HIS A 323 " ideal model delta sigma weight residual 109.80 115.69 -5.89 1.23e+00 6.61e-01 2.29e+01 angle pdb=" C SER B 433 " pdb=" CA SER B 433 " pdb=" CB SER B 433 " ideal model delta sigma weight residual 116.34 110.15 6.19 1.40e+00 5.10e-01 1.95e+01 angle pdb=" N VAL A 325 " pdb=" CA VAL A 325 " pdb=" C VAL A 325 " ideal model delta sigma weight residual 112.98 107.51 5.47 1.25e+00 6.40e-01 1.91e+01 angle pdb=" O ALA B 491 " pdb=" C ALA B 491 " pdb=" N ASN B 492 " ideal model delta sigma weight residual 120.71 124.44 -3.73 9.00e-01 1.23e+00 1.72e+01 angle pdb=" N ALA A 320 " pdb=" CA ALA A 320 " pdb=" C ALA A 320 " ideal model delta sigma weight residual 114.12 108.56 5.56 1.39e+00 5.18e-01 1.60e+01 ... (remaining 6620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2720 16.75 - 33.51: 127 33.51 - 50.26: 23 50.26 - 67.01: 2 67.01 - 83.76: 3 Dihedral angle restraints: 2875 sinusoidal: 1154 harmonic: 1721 Sorted by residual: dihedral pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " pdb=" NH1 ARG A 321 " ideal model delta sinusoidal sigma weight residual 0.00 -83.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CD ARG B 509 " pdb=" NE ARG B 509 " pdb=" CZ ARG B 509 " pdb=" NH1 ARG B 509 " ideal model delta sinusoidal sigma weight residual 0.00 76.73 -76.73 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CA VAL B 419 " pdb=" C VAL B 419 " pdb=" N TRP B 420 " pdb=" CA TRP B 420 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 559 0.056 - 0.112: 127 0.112 - 0.167: 31 0.167 - 0.223: 5 0.223 - 0.278: 3 Chirality restraints: 725 Sorted by residual: chirality pdb=" C1 GLA D 3 " pdb=" O3 GLA D 1 " pdb=" C2 GLA D 3 " pdb=" O5 GLA D 3 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 GLA C 3 " pdb=" O3 GLA C 1 " pdb=" C2 GLA C 3 " pdb=" O5 GLA C 3 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.90e+02 chirality pdb=" C1 FUC C 2 " pdb=" O2 GLA C 1 " pdb=" C2 FUC C 2 " pdb=" O5 FUC C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 ... (remaining 722 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -1.105 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG A 321 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 509 " 1.071 9.50e-02 1.11e+02 4.80e-01 1.39e+02 pdb=" NE ARG B 509 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 509 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 509 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 509 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 434 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C SER A 434 " 0.023 2.00e-02 2.50e+03 pdb=" O SER A 434 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 435 " -0.008 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 3 2.19 - 2.87: 1846 2.87 - 3.55: 5924 3.55 - 4.22: 10989 4.22 - 4.90: 19051 Nonbonded interactions: 37813 Sorted by model distance: nonbonded pdb=" CA ASP A 351 " pdb=" OD1 ASP A 357 " model vdw 1.517 3.470 nonbonded pdb=" O TRP A 346 " pdb=" OD1 ASP A 347 " model vdw 1.803 3.040 nonbonded pdb=" O TRP B 346 " pdb=" OD1 ASP B 347 " model vdw 1.861 3.040 nonbonded pdb=" ND2 ASN A 437 " pdb=" O5 GLA C 3 " model vdw 2.224 3.120 nonbonded pdb=" N ASP A 351 " pdb=" OD1 ASP A 357 " model vdw 2.239 3.120 ... (remaining 37808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 209 through 364 or (resid 365 and (name N or name CA or na \ me C or name O )) or resid 366 through 516)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.090 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.005 0.056 4837 Z= 0.317 Angle : 0.756 6.700 6637 Z= 0.446 Chirality : 0.054 0.278 725 Planarity : 0.024 0.495 855 Dihedral : 10.234 83.762 1789 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.39 % Allowed : 7.16 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.31), residues: 598 helix: -1.20 (0.81), residues: 36 sheet: -1.61 (0.41), residues: 170 loop : -2.14 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.014 0.001 TYR B 365 PHE 0.017 0.002 PHE B 272 TRP 0.010 0.001 TRP B 404 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 4833) covalent geometry : angle 0.75294 ( 6625) hydrogen bonds : bond 0.21880 ( 91) hydrogen bonds : angle 9.39967 ( 234) link_ALPHA1-3 : bond 0.01090 ( 2) link_ALPHA1-3 : angle 2.29761 ( 6) link_BETA1-2 : bond 0.00504 ( 2) link_BETA1-2 : angle 1.26207 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.105 Fit side-chains REVERT: B 222 VAL cc_start: 0.8479 (t) cc_final: 0.8089 (p) REVERT: B 405 ASP cc_start: 0.7870 (t0) cc_final: 0.7643 (t0) REVERT: B 514 VAL cc_start: 0.8888 (p) cc_final: 0.8668 (m) outliers start: 12 outliers final: 3 residues processed: 109 average time/residue: 0.0516 time to fit residues: 7.3040 Evaluate side-chains 74 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123501 restraints weight = 5374.767| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.95 r_work: 0.3232 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 4837 Z= 0.325 Angle : 0.835 11.636 6637 Z= 0.425 Chirality : 0.055 0.178 725 Planarity : 0.006 0.047 855 Dihedral : 6.222 53.607 777 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.98 % Allowed : 12.33 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.30), residues: 598 helix: -2.93 (0.71), residues: 24 sheet: -2.25 (0.43), residues: 154 loop : -2.30 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 321 TYR 0.025 0.002 TYR B 365 PHE 0.027 0.003 PHE A 272 TRP 0.019 0.002 TRP A 346 HIS 0.006 0.003 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 4833) covalent geometry : angle 0.82974 ( 6625) hydrogen bonds : bond 0.04905 ( 91) hydrogen bonds : angle 8.02366 ( 234) link_ALPHA1-3 : bond 0.00361 ( 2) link_ALPHA1-3 : angle 1.41814 ( 6) link_BETA1-2 : bond 0.00815 ( 2) link_BETA1-2 : angle 2.92391 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.104 Fit side-chains REVERT: B 514 VAL cc_start: 0.8906 (p) cc_final: 0.8655 (m) outliers start: 20 outliers final: 14 residues processed: 86 average time/residue: 0.0441 time to fit residues: 5.1022 Evaluate side-chains 81 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130247 restraints weight = 5293.281| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.93 r_work: 0.3310 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4837 Z= 0.132 Angle : 0.594 7.756 6637 Z= 0.303 Chirality : 0.047 0.183 725 Planarity : 0.004 0.033 855 Dihedral : 5.025 28.731 777 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.98 % Allowed : 12.52 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.30), residues: 598 helix: -2.44 (0.76), residues: 24 sheet: -1.76 (0.40), residues: 170 loop : -2.21 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 453 TYR 0.014 0.001 TYR B 365 PHE 0.020 0.002 PHE B 272 TRP 0.010 0.001 TRP B 404 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4833) covalent geometry : angle 0.58813 ( 6625) hydrogen bonds : bond 0.03640 ( 91) hydrogen bonds : angle 7.40259 ( 234) link_ALPHA1-3 : bond 0.00854 ( 2) link_ALPHA1-3 : angle 1.23773 ( 6) link_BETA1-2 : bond 0.01031 ( 2) link_BETA1-2 : angle 2.69679 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.151 Fit side-chains REVERT: A 354 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6280 (mm) REVERT: A 356 LEU cc_start: 0.8380 (pp) cc_final: 0.8163 (pp) REVERT: A 431 SER cc_start: 0.8904 (t) cc_final: 0.8595 (p) REVERT: B 514 VAL cc_start: 0.8920 (p) cc_final: 0.8686 (m) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.0490 time to fit residues: 5.4813 Evaluate side-chains 77 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 477 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.0270 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS B 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127215 restraints weight = 5317.906| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.93 r_work: 0.3285 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4837 Z= 0.185 Angle : 0.632 7.876 6637 Z= 0.321 Chirality : 0.048 0.164 725 Planarity : 0.004 0.035 855 Dihedral : 5.078 24.730 777 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.57 % Allowed : 11.93 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.30), residues: 598 helix: -2.53 (0.76), residues: 24 sheet: -2.32 (0.37), residues: 174 loop : -2.12 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.018 0.001 TYR B 365 PHE 0.019 0.002 PHE B 272 TRP 0.011 0.001 TRP B 404 HIS 0.005 0.002 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 4833) covalent geometry : angle 0.62644 ( 6625) hydrogen bonds : bond 0.03753 ( 91) hydrogen bonds : angle 7.35267 ( 234) link_ALPHA1-3 : bond 0.00603 ( 2) link_ALPHA1-3 : angle 1.30726 ( 6) link_BETA1-2 : bond 0.01021 ( 2) link_BETA1-2 : angle 2.59769 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.156 Fit side-chains REVERT: A 354 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6315 (mm) REVERT: A 363 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 431 SER cc_start: 0.8917 (t) cc_final: 0.8618 (p) REVERT: B 257 ILE cc_start: 0.8720 (tp) cc_final: 0.8456 (tp) REVERT: B 514 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8666 (m) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.0426 time to fit residues: 4.9772 Evaluate side-chains 82 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS B 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130580 restraints weight = 5317.847| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.85 r_work: 0.3329 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4837 Z= 0.109 Angle : 0.556 7.451 6637 Z= 0.278 Chirality : 0.045 0.153 725 Planarity : 0.004 0.030 855 Dihedral : 4.571 22.196 777 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.58 % Allowed : 11.93 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.31), residues: 598 helix: -2.37 (0.80), residues: 24 sheet: -1.79 (0.39), residues: 182 loop : -2.06 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 453 TYR 0.014 0.001 TYR B 365 PHE 0.018 0.002 PHE B 272 TRP 0.008 0.001 TRP A 404 HIS 0.001 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4833) covalent geometry : angle 0.55048 ( 6625) hydrogen bonds : bond 0.02912 ( 91) hydrogen bonds : angle 7.00406 ( 234) link_ALPHA1-3 : bond 0.00676 ( 2) link_ALPHA1-3 : angle 1.29939 ( 6) link_BETA1-2 : bond 0.01061 ( 2) link_BETA1-2 : angle 2.31320 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.107 Fit side-chains REVERT: A 354 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6202 (mm) REVERT: A 431 SER cc_start: 0.8882 (t) cc_final: 0.8582 (p) REVERT: B 257 ILE cc_start: 0.8668 (tp) cc_final: 0.8398 (tp) REVERT: B 514 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (m) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.0411 time to fit residues: 4.6287 Evaluate side-chains 76 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129768 restraints weight = 5430.109| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.87 r_work: 0.3315 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4837 Z= 0.122 Angle : 0.555 7.092 6637 Z= 0.279 Chirality : 0.046 0.154 725 Planarity : 0.004 0.029 855 Dihedral : 4.541 23.145 777 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.37 % Allowed : 11.93 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.31), residues: 598 helix: -2.41 (0.79), residues: 24 sheet: -1.75 (0.39), residues: 182 loop : -2.02 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.016 0.001 TYR B 365 PHE 0.018 0.002 PHE B 272 TRP 0.009 0.001 TRP A 404 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4833) covalent geometry : angle 0.55043 ( 6625) hydrogen bonds : bond 0.03027 ( 91) hydrogen bonds : angle 6.95282 ( 234) link_ALPHA1-3 : bond 0.00631 ( 2) link_ALPHA1-3 : angle 1.33460 ( 6) link_BETA1-2 : bond 0.00999 ( 2) link_BETA1-2 : angle 2.24127 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.132 Fit side-chains REVERT: A 354 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6196 (mm) REVERT: A 431 SER cc_start: 0.8884 (t) cc_final: 0.8575 (p) REVERT: B 257 ILE cc_start: 0.8645 (tp) cc_final: 0.8390 (tp) REVERT: B 514 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8622 (m) outliers start: 22 outliers final: 16 residues processed: 79 average time/residue: 0.0485 time to fit residues: 5.4025 Evaluate side-chains 80 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129028 restraints weight = 5296.745| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.87 r_work: 0.3305 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4837 Z= 0.127 Angle : 0.556 6.593 6637 Z= 0.281 Chirality : 0.046 0.155 725 Planarity : 0.004 0.030 855 Dihedral : 4.539 24.269 777 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.17 % Allowed : 12.72 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.31), residues: 598 helix: -2.40 (0.79), residues: 24 sheet: -2.06 (0.40), residues: 164 loop : -1.93 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.016 0.001 TYR B 365 PHE 0.017 0.002 PHE B 272 TRP 0.011 0.001 TRP A 404 HIS 0.002 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4833) covalent geometry : angle 0.55140 ( 6625) hydrogen bonds : bond 0.03129 ( 91) hydrogen bonds : angle 6.93616 ( 234) link_ALPHA1-3 : bond 0.00569 ( 2) link_ALPHA1-3 : angle 1.29547 ( 6) link_BETA1-2 : bond 0.00981 ( 2) link_BETA1-2 : angle 2.12461 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.120 Fit side-chains REVERT: A 354 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6207 (mm) REVERT: A 431 SER cc_start: 0.8878 (t) cc_final: 0.8588 (p) REVERT: B 257 ILE cc_start: 0.8679 (tp) cc_final: 0.8432 (tp) REVERT: B 514 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8629 (m) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.0500 time to fit residues: 5.3987 Evaluate side-chains 76 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS B 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126466 restraints weight = 5396.814| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.88 r_work: 0.3273 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4837 Z= 0.165 Angle : 0.603 9.099 6637 Z= 0.304 Chirality : 0.047 0.163 725 Planarity : 0.004 0.035 855 Dihedral : 4.792 25.600 777 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.77 % Allowed : 12.52 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.31), residues: 598 helix: -2.56 (0.75), residues: 24 sheet: -2.20 (0.38), residues: 174 loop : -1.94 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.018 0.001 TYR B 365 PHE 0.018 0.002 PHE B 272 TRP 0.014 0.001 TRP A 404 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4833) covalent geometry : angle 0.59847 ( 6625) hydrogen bonds : bond 0.03470 ( 91) hydrogen bonds : angle 7.09771 ( 234) link_ALPHA1-3 : bond 0.00469 ( 2) link_ALPHA1-3 : angle 1.33982 ( 6) link_BETA1-2 : bond 0.00901 ( 2) link_BETA1-2 : angle 2.09180 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: A 354 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6223 (mm) REVERT: A 431 SER cc_start: 0.8884 (t) cc_final: 0.8595 (p) REVERT: B 257 ILE cc_start: 0.8640 (tp) cc_final: 0.8391 (tp) REVERT: B 514 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8595 (m) outliers start: 24 outliers final: 19 residues processed: 78 average time/residue: 0.0595 time to fit residues: 6.3421 Evaluate side-chains 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129722 restraints weight = 5214.506| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.94 r_work: 0.3311 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4837 Z= 0.116 Angle : 0.555 8.596 6637 Z= 0.280 Chirality : 0.046 0.175 725 Planarity : 0.004 0.029 855 Dihedral : 4.586 24.904 777 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.57 % Allowed : 12.33 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.31), residues: 598 helix: -2.48 (0.77), residues: 24 sheet: -2.18 (0.40), residues: 164 loop : -1.90 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.015 0.001 TYR B 365 PHE 0.018 0.002 PHE B 272 TRP 0.012 0.001 TRP A 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4833) covalent geometry : angle 0.55107 ( 6625) hydrogen bonds : bond 0.03072 ( 91) hydrogen bonds : angle 6.96929 ( 234) link_ALPHA1-3 : bond 0.00555 ( 2) link_ALPHA1-3 : angle 1.28759 ( 6) link_BETA1-2 : bond 0.00906 ( 2) link_BETA1-2 : angle 1.98080 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.191 Fit side-chains REVERT: A 354 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6271 (mm) REVERT: A 431 SER cc_start: 0.8916 (t) cc_final: 0.8640 (p) REVERT: B 257 ILE cc_start: 0.8679 (tp) cc_final: 0.8433 (tp) REVERT: B 514 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (m) outliers start: 23 outliers final: 19 residues processed: 74 average time/residue: 0.0445 time to fit residues: 4.8806 Evaluate side-chains 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 400 CYS Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.128503 restraints weight = 5252.026| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.93 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4837 Z= 0.140 Angle : 0.574 8.639 6637 Z= 0.290 Chirality : 0.046 0.169 725 Planarity : 0.004 0.033 855 Dihedral : 4.660 25.752 777 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.98 % Allowed : 12.72 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.31), residues: 598 helix: -2.55 (0.76), residues: 24 sheet: -2.03 (0.44), residues: 146 loop : -1.91 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.017 0.001 TYR B 365 PHE 0.018 0.002 PHE B 272 TRP 0.013 0.001 TRP A 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4833) covalent geometry : angle 0.57053 ( 6625) hydrogen bonds : bond 0.03264 ( 91) hydrogen bonds : angle 7.00563 ( 234) link_ALPHA1-3 : bond 0.00499 ( 2) link_ALPHA1-3 : angle 1.32556 ( 6) link_BETA1-2 : bond 0.00882 ( 2) link_BETA1-2 : angle 1.94768 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.103 Fit side-chains REVERT: A 354 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6284 (mm) REVERT: A 431 SER cc_start: 0.8914 (t) cc_final: 0.8630 (p) REVERT: B 257 ILE cc_start: 0.8647 (tp) cc_final: 0.8398 (tp) REVERT: B 514 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (m) outliers start: 20 outliers final: 18 residues processed: 74 average time/residue: 0.0443 time to fit residues: 4.7038 Evaluate side-chains 78 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132857 restraints weight = 5225.048| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.02 r_work: 0.3338 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4837 Z= 0.093 Angle : 0.519 8.230 6637 Z= 0.260 Chirality : 0.044 0.151 725 Planarity : 0.004 0.029 855 Dihedral : 4.256 24.125 777 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.58 % Allowed : 13.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.31), residues: 598 helix: -2.15 (0.85), residues: 24 sheet: -1.59 (0.43), residues: 164 loop : -1.87 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 286 TYR 0.013 0.001 TYR B 365 PHE 0.017 0.001 PHE B 272 TRP 0.011 0.001 TRP A 404 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4833) covalent geometry : angle 0.51503 ( 6625) hydrogen bonds : bond 0.02628 ( 91) hydrogen bonds : angle 6.75773 ( 234) link_ALPHA1-3 : bond 0.00625 ( 2) link_ALPHA1-3 : angle 1.26911 ( 6) link_BETA1-2 : bond 0.00908 ( 2) link_BETA1-2 : angle 1.72180 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1106.34 seconds wall clock time: 19 minutes 37.08 seconds (1177.08 seconds total)