Starting phenix.real_space_refine on Thu Jul 2 19:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tok_41454/07_2026/8tok_41454.map" } resolution = 3.84 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 40 5.16 5 C 6494 2.51 5 N 1648 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4952 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 29, 'TRANS': 599} Chain breaks: 6 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 4, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 3.33, per 1000 atoms: 0.34 Number of scatterers: 9908 At special positions: 0 Unit cell: (128.31, 104.65, 101.92, 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) Ca 4 19.99 S 40 16.00 O 1722 8.00 N 1648 7.00 C 6494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 331.5 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 73.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 72 through 91 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 124 Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.025A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.960A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.959A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.522A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.924A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 4.047A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 330 through 357 Proline residue: A 341 - end of helix removed outlier: 3.870A pdb=" N MET A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 4.120A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 Processing helix chain 'A' and resid 431 through 466 removed outlier: 4.440A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.775A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.749A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 583 removed outlier: 3.527A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.524A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 4.039A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 72 through 91 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 135 through 139 removed outlier: 4.023A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.960A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.959A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.521A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.924A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 4.047A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 330 through 357 Proline residue: B 341 - end of helix removed outlier: 3.869A pdb=" N MET B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 4.120A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 416 Processing helix chain 'B' and resid 431 through 466 removed outlier: 4.440A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 482 through 495 Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.773A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.749A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.527A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.524A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 removed outlier: 4.039A pdb=" N LEU B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 701 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.966A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.967A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2016 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: 1.10 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3095 1.34 - 1.46: 2464 1.46 - 1.58: 4547 1.58 - 1.70: 4 1.70 - 1.81: 66 Bond restraints: 10176 Sorted by residual: bond pdb=" CB PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 1.492 1.647 -0.155 5.00e-02 4.00e+02 9.57e+00 bond pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.44e+00 bond pdb=" CB PRO A 596 " pdb=" CG PRO A 596 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.20e+00 bond pdb=" CB PRO B 596 " pdb=" CG PRO B 596 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.17e+00 bond pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.64e+00 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 13800 3.41 - 6.83: 36 6.83 - 10.24: 8 10.24 - 13.66: 2 13.66 - 17.07: 2 Bond angle restraints: 13848 Sorted by residual: angle pdb=" CA PRO B 202 " pdb=" N PRO B 202 " pdb=" CD PRO B 202 " ideal model delta sigma weight residual 112.00 94.93 17.07 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO A 202 " pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 112.00 94.99 17.01 1.40e+00 5.10e-01 1.48e+02 angle pdb=" N PRO A 202 " pdb=" CD PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 103.20 95.15 8.05 1.50e+00 4.44e-01 2.88e+01 angle pdb=" N PRO B 202 " pdb=" CD PRO B 202 " pdb=" CG PRO B 202 " ideal model delta sigma weight residual 103.20 95.18 8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" CA PRO B 596 " pdb=" N PRO B 596 " pdb=" CD PRO B 596 " ideal model delta sigma weight residual 112.00 107.00 5.00 1.40e+00 5.10e-01 1.28e+01 ... (remaining 13843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4932 17.12 - 34.23: 736 34.23 - 51.35: 203 51.35 - 68.46: 27 68.46 - 85.58: 12 Dihedral angle restraints: 5910 sinusoidal: 2240 harmonic: 3670 Sorted by residual: dihedral pdb=" CA VAL A 453 " pdb=" C VAL A 453 " pdb=" N VAL A 454 " pdb=" CA VAL A 454 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA VAL B 453 " pdb=" C VAL B 453 " pdb=" N VAL B 454 " pdb=" CA VAL B 454 " ideal model delta harmonic sigma weight residual 180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CG ARG A 548 " pdb=" CD ARG A 548 " pdb=" NE ARG A 548 " pdb=" CZ ARG A 548 " ideal model delta sinusoidal sigma weight residual -90.00 -133.76 43.76 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1091 0.031 - 0.061: 309 0.061 - 0.092: 94 0.092 - 0.123: 48 0.123 - 0.154: 10 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA PRO B 402 " pdb=" N PRO B 402 " pdb=" C PRO B 402 " pdb=" CB PRO B 402 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 1549 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 201 " 0.096 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO A 202 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 201 " -0.096 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO B 202 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 402 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.038 5.00e-02 4.00e+02 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 537 2.74 - 3.28: 9826 3.28 - 3.82: 16631 3.82 - 4.36: 16220 4.36 - 4.90: 30638 Nonbonded interactions: 73852 Sorted by model distance: nonbonded pdb=" O SER A 165 " pdb=" OG SER A 165 " model vdw 2.195 3.040 nonbonded pdb=" O SER B 165 " pdb=" OG SER B 165 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.236 3.040 nonbonded pdb=" O TRP A 407 " pdb=" OG1 THR A 410 " model vdw 2.271 3.040 ... (remaining 73847 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: 2.090 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.004 0.155 10176 Z= 0.133 Angle : 0.602 17.072 13848 Z= 0.337 Chirality : 0.037 0.154 1552 Planarity : 0.006 0.132 1738 Dihedral : 17.557 85.575 3526 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 29.63 % Favored : 70.37 % 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: 1.87 (0.24), residues: 1230 helix: 2.60 (0.17), residues: 832 sheet: -2.23 (0.79), residues: 48 loop : -1.77 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 249 TYR 0.006 0.001 TYR B 26 PHE 0.033 0.001 PHE B 315 TRP 0.012 0.001 TRP A 521 HIS 0.003 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.13 (10176) covalent geometry : angle 0.60191 / 0.34 (13848) hydrogen bonds : bond 0.13969 / 9.59 ( 682) hydrogen bonds : angle 4.75697 / 3.45 ( 2016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0661 time to fit residues: 9.1838 Evaluate side-chains 87 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 445 GLN A 611 HIS B 79 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS B 445 GLN B 611 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115263 restraints weight = 13308.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114401 restraints weight = 19808.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115187 restraints weight = 17502.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114764 restraints weight = 13206.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115117 restraints weight = 13220.249| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10176 Z= 0.147 Angle : 0.539 10.182 13848 Z= 0.278 Chirality : 0.039 0.154 1552 Planarity : 0.004 0.064 1738 Dihedral : 3.560 19.131 1340 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.76 % Allowed : 30.02 % Favored : 67.22 % 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: 2.19 (0.25), residues: 1230 helix: 2.84 (0.17), residues: 862 sheet: -1.36 (0.68), residues: 68 loop : -2.27 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 621 TYR 0.010 0.001 TYR A 26 PHE 0.014 0.001 PHE B 379 TRP 0.012 0.001 TRP B 533 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10176) covalent geometry : angle 0.53855 / 0.28 (13848) hydrogen bonds : bond 0.05157 / 3.61 ( 682) hydrogen bonds : angle 3.58673 / 2.60 ( 2016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.207 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.0671 time to fit residues: 12.1369 Evaluate side-chains 107 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.0970 chunk 108 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 0.0020 chunk 40 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.149946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120277 restraints weight = 13257.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119899 restraints weight = 16580.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121038 restraints weight = 14384.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121095 restraints weight = 10822.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121334 restraints weight = 10578.476| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10176 Z= 0.102 Angle : 0.495 9.067 13848 Z= 0.251 Chirality : 0.037 0.150 1552 Planarity : 0.004 0.052 1738 Dihedral : 3.481 19.726 1340 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.67 % Allowed : 29.72 % Favored : 68.60 % 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: 2.42 (0.25), residues: 1230 helix: 2.98 (0.17), residues: 874 sheet: -1.48 (0.68), residues: 68 loop : -2.23 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 57 TYR 0.009 0.001 TYR A 188 PHE 0.010 0.001 PHE B 315 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.000 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10176) covalent geometry : angle 0.49515 / 0.25 (13848) hydrogen bonds : bond 0.03692 / 2.57 ( 682) hydrogen bonds : angle 3.29652 / 2.38 ( 2016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.337 Fit side-chains REVERT: A 122 MET cc_start: 0.8652 (ttm) cc_final: 0.8426 (ttm) REVERT: A 509 MET cc_start: 0.8197 (mmp) cc_final: 0.7824 (mmp) REVERT: B 122 MET cc_start: 0.8625 (ttm) cc_final: 0.8367 (ttm) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.0657 time to fit residues: 11.1566 Evaluate side-chains 106 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116944 restraints weight = 13560.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116259 restraints weight = 18842.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117369 restraints weight = 16549.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.116411 restraints weight = 14477.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116788 restraints weight = 12417.247| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10176 Z= 0.123 Angle : 0.503 8.745 13848 Z= 0.257 Chirality : 0.038 0.148 1552 Planarity : 0.003 0.048 1738 Dihedral : 3.405 19.167 1340 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.76 % Allowed : 30.02 % Favored : 67.22 % 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: 2.34 (0.25), residues: 1230 helix: 2.91 (0.17), residues: 874 sheet: -1.42 (0.66), residues: 68 loop : -2.25 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.009 0.001 TYR A 26 PHE 0.017 0.001 PHE B 379 TRP 0.010 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (10176) covalent geometry : angle 0.50266 / 0.26 (13848) hydrogen bonds : bond 0.04471 / 3.13 ( 682) hydrogen bonds : angle 3.25873 / 2.36 ( 2016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.278 Fit side-chains REVERT: A 122 MET cc_start: 0.8669 (ttm) cc_final: 0.8353 (ttm) REVERT: A 491 GLU cc_start: 0.6009 (tp30) cc_final: 0.5807 (tp30) REVERT: B 122 MET cc_start: 0.8679 (ttm) cc_final: 0.8305 (ttm) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.0672 time to fit residues: 12.1118 Evaluate side-chains 108 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** 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 = 0.3550 r_free = 0.3550 target = 0.143712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112974 restraints weight = 13606.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112665 restraints weight = 17434.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113764 restraints weight = 13619.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113579 restraints weight = 12665.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114025 restraints weight = 10764.879| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10176 Z= 0.128 Angle : 0.527 8.124 13848 Z= 0.267 Chirality : 0.038 0.157 1552 Planarity : 0.003 0.030 1738 Dihedral : 3.428 19.505 1340 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.95 % Allowed : 29.63 % Favored : 67.42 % 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: 2.27 (0.25), residues: 1230 helix: 2.87 (0.17), residues: 874 sheet: -1.54 (0.65), residues: 68 loop : -2.32 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 549 TYR 0.009 0.001 TYR B 26 PHE 0.015 0.001 PHE B 406 TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10176) covalent geometry : angle 0.52690 / 0.27 (13848) hydrogen bonds : bond 0.04527 / 3.17 ( 682) hydrogen bonds : angle 3.26899 / 2.36 ( 2016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.464 Fit side-chains REVERT: A 122 MET cc_start: 0.8665 (ttm) cc_final: 0.8307 (ttm) REVERT: A 219 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 521 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7192 (t60) REVERT: B 122 MET cc_start: 0.8674 (ttm) cc_final: 0.8290 (ttm) REVERT: B 219 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 491 GLU cc_start: 0.6103 (tp30) cc_final: 0.5873 (tp30) REVERT: B 495 LEU cc_start: 0.7773 (mp) cc_final: 0.7470 (mp) REVERT: B 521 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7191 (t60) outliers start: 30 outliers final: 21 residues processed: 112 average time/residue: 0.0627 time to fit residues: 10.9222 Evaluate side-chains 109 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 GLN ** B 359 ASN ** 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 = 0.3504 r_free = 0.3504 target = 0.139680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109890 restraints weight = 13714.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109960 restraints weight = 15903.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110277 restraints weight = 14035.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110764 restraints weight = 12261.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110827 restraints weight = 11523.510| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10176 Z= 0.165 Angle : 0.557 8.050 13848 Z= 0.287 Chirality : 0.039 0.146 1552 Planarity : 0.003 0.028 1738 Dihedral : 3.562 19.313 1340 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.54 % Allowed : 29.53 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.25), residues: 1230 helix: 2.73 (0.17), residues: 874 sheet: -1.50 (0.63), residues: 68 loop : -2.38 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 549 TYR 0.010 0.001 TYR B 26 PHE 0.019 0.001 PHE A 379 TRP 0.010 0.001 TRP B 695 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.16 (10176) covalent geometry : angle 0.55664 / 0.29 (13848) hydrogen bonds : bond 0.05540 / 3.89 ( 682) hydrogen bonds : angle 3.38247 / 2.44 ( 2016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.230 Fit side-chains REVERT: A 219 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 521 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7185 (t60) REVERT: B 122 MET cc_start: 0.8722 (ttm) cc_final: 0.8299 (ttm) REVERT: B 219 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7919 (tt) REVERT: B 521 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7254 (t60) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.0654 time to fit residues: 12.5189 Evaluate side-chains 117 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 359 ASN ** 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 = 0.3526 r_free = 0.3526 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110462 restraints weight = 13617.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110142 restraints weight = 17686.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110983 restraints weight = 14405.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111268 restraints weight = 11753.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111308 restraints weight = 11179.910| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.132 Angle : 0.527 7.441 13848 Z= 0.270 Chirality : 0.038 0.143 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.536 19.136 1340 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.44 % Allowed : 29.43 % Favored : 67.13 % 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: 2.15 (0.25), residues: 1230 helix: 2.76 (0.17), residues: 874 sheet: -2.27 (0.71), residues: 48 loop : -2.14 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 549 TYR 0.010 0.001 TYR B 26 PHE 0.017 0.001 PHE A 205 TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10176) covalent geometry : angle 0.52664 / 0.27 (13848) hydrogen bonds : bond 0.04856 / 3.40 ( 682) hydrogen bonds : angle 3.30287 / 2.38 ( 2016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.269 Fit side-chains REVERT: A 75 LEU cc_start: 0.8287 (mt) cc_final: 0.7775 (tt) REVERT: A 122 MET cc_start: 0.8685 (ttm) cc_final: 0.8380 (ttm) REVERT: A 219 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7810 (tt) REVERT: A 521 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.7192 (t60) REVERT: B 33 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7741 (mtm180) REVERT: B 122 MET cc_start: 0.8700 (ttm) cc_final: 0.8296 (ttm) REVERT: B 219 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7815 (tt) REVERT: B 491 GLU cc_start: 0.6236 (tp30) cc_final: 0.6018 (tp30) REVERT: B 495 LEU cc_start: 0.7882 (mp) cc_final: 0.7553 (mp) REVERT: B 521 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7237 (t60) outliers start: 35 outliers final: 27 residues processed: 119 average time/residue: 0.0633 time to fit residues: 11.4647 Evaluate side-chains 115 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 359 ASN ** 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 = 0.3552 r_free = 0.3552 target = 0.143764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113165 restraints weight = 13438.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112885 restraints weight = 16299.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114376 restraints weight = 13747.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114172 restraints weight = 11196.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114428 restraints weight = 9872.856| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10176 Z= 0.115 Angle : 0.513 7.775 13848 Z= 0.261 Chirality : 0.037 0.142 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.476 19.031 1340 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.76 % Allowed : 30.31 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.25), residues: 1230 helix: 2.86 (0.17), residues: 874 sheet: -2.17 (0.73), residues: 48 loop : -2.14 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 621 TYR 0.009 0.001 TYR B 26 PHE 0.013 0.001 PHE A 205 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (10176) covalent geometry : angle 0.51254 / 0.26 (13848) hydrogen bonds : bond 0.04261 / 2.98 ( 682) hydrogen bonds : angle 3.19090 / 2.31 ( 2016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.265 Fit side-chains REVERT: A 75 LEU cc_start: 0.8259 (mt) cc_final: 0.7609 (tp) REVERT: A 122 MET cc_start: 0.8672 (ttm) cc_final: 0.8343 (ttm) REVERT: A 219 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 495 LEU cc_start: 0.7795 (mp) cc_final: 0.7555 (mt) REVERT: A 521 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7224 (t60) REVERT: B 122 MET cc_start: 0.8648 (ttm) cc_final: 0.8265 (ttm) REVERT: B 219 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 309 CYS cc_start: 0.7004 (m) cc_final: 0.6527 (m) REVERT: B 484 GLU cc_start: 0.8340 (pm20) cc_final: 0.7579 (mm-30) REVERT: B 491 GLU cc_start: 0.6224 (tp30) cc_final: 0.6010 (tp30) REVERT: B 495 LEU cc_start: 0.7753 (mp) cc_final: 0.7436 (mp) REVERT: B 521 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.7098 (t60) outliers start: 28 outliers final: 23 residues processed: 118 average time/residue: 0.0611 time to fit residues: 10.9167 Evaluate side-chains 114 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** 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 = 0.3482 r_free = 0.3482 target = 0.137571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109605 restraints weight = 13674.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107821 restraints weight = 21642.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108716 restraints weight = 21220.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108604 restraints weight = 16119.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108945 restraints weight = 14511.727| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10176 Z= 0.184 Angle : 0.581 10.099 13848 Z= 0.299 Chirality : 0.039 0.145 1552 Planarity : 0.003 0.028 1738 Dihedral : 3.605 18.862 1340 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.74 % Allowed : 29.33 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.24), residues: 1230 helix: 2.62 (0.17), residues: 874 sheet: -2.20 (0.71), residues: 48 loop : -2.21 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 549 TYR 0.011 0.001 TYR B 26 PHE 0.021 0.001 PHE A 205 TRP 0.009 0.001 TRP A 159 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (10176) covalent geometry : angle 0.58132 / 0.30 (13848) hydrogen bonds : bond 0.05847 / 4.10 ( 682) hydrogen bonds : angle 3.44349 / 2.48 ( 2016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.261 Fit side-chains REVERT: A 75 LEU cc_start: 0.8292 (mt) cc_final: 0.7858 (tt) REVERT: A 219 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8049 (tt) REVERT: A 521 TRP cc_start: 0.8211 (OUTLIER) cc_final: 0.7153 (t60) REVERT: B 75 LEU cc_start: 0.8227 (mt) cc_final: 0.7762 (tt) REVERT: B 122 MET cc_start: 0.8740 (ttm) cc_final: 0.8354 (ttm) REVERT: B 219 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (tt) REVERT: B 484 GLU cc_start: 0.8257 (pm20) cc_final: 0.7634 (mm-30) REVERT: B 495 LEU cc_start: 0.8178 (mp) cc_final: 0.7854 (mp) REVERT: B 521 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.7158 (t60) outliers start: 38 outliers final: 30 residues processed: 125 average time/residue: 0.0702 time to fit residues: 13.2338 Evaluate side-chains 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 359 ASN ** 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 = 0.3514 r_free = 0.3514 target = 0.140545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112873 restraints weight = 13518.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111594 restraints weight = 21146.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113086 restraints weight = 19547.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112566 restraints weight = 14390.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112905 restraints weight = 14992.528| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.135 Angle : 0.546 10.835 13848 Z= 0.277 Chirality : 0.038 0.145 1552 Planarity : 0.003 0.028 1738 Dihedral : 3.585 18.901 1340 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.15 % Allowed : 29.82 % Favored : 67.03 % 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: 2.11 (0.25), residues: 1230 helix: 2.74 (0.17), residues: 874 sheet: -2.21 (0.72), residues: 48 loop : -2.21 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 549 TYR 0.010 0.001 TYR A 26 PHE 0.015 0.001 PHE A 205 TRP 0.011 0.001 TRP B 235 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (10176) covalent geometry : angle 0.54565 / 0.28 (13848) hydrogen bonds : bond 0.04883 / 3.42 ( 682) hydrogen bonds : angle 3.30876 / 2.39 ( 2016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.375 Fit side-chains REVERT: A 75 LEU cc_start: 0.8259 (mt) cc_final: 0.7661 (tp) REVERT: A 219 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 495 LEU cc_start: 0.7995 (mp) cc_final: 0.7599 (mp) REVERT: A 521 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.7149 (t60) REVERT: B 75 LEU cc_start: 0.8194 (mt) cc_final: 0.7692 (tt) REVERT: B 122 MET cc_start: 0.8721 (ttm) cc_final: 0.8314 (ttm) REVERT: B 219 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 484 GLU cc_start: 0.8201 (pm20) cc_final: 0.7562 (mm-30) REVERT: B 491 GLU cc_start: 0.6216 (tp30) cc_final: 0.6015 (tp30) REVERT: B 495 LEU cc_start: 0.7960 (mp) cc_final: 0.7642 (mp) REVERT: B 521 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.7154 (t60) outliers start: 32 outliers final: 26 residues processed: 121 average time/residue: 0.0661 time to fit residues: 12.3394 Evaluate side-chains 121 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 521 TRP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 521 TRP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain B residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.141629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113700 restraints weight = 13487.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112485 restraints weight = 22291.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113533 restraints weight = 19357.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113098 restraints weight = 14238.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113553 restraints weight = 13171.578| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.130 Angle : 0.545 10.968 13848 Z= 0.276 Chirality : 0.038 0.152 1552 Planarity : 0.003 0.029 1738 Dihedral : 3.549 18.985 1340 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.95 % Allowed : 30.12 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.25), residues: 1230 helix: 2.76 (0.17), residues: 874 sheet: -2.20 (0.72), residues: 48 loop : -2.18 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.010 0.001 TYR B 26 PHE 0.018 0.001 PHE B 205 TRP 0.011 0.001 TRP B 235 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10176) covalent geometry : angle 0.54534 / 0.28 (13848) hydrogen bonds : bond 0.04774 / 3.34 ( 682) hydrogen bonds : angle 3.28836 / 2.38 ( 2016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.94 seconds wall clock time: 20 minutes 37.07 seconds (1237.07 seconds total)