Starting phenix.real_space_refine on Wed Mar 4 06:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.map" model { file = "/net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v9z_21132/03_2026/6v9z_21132.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.046 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 58 5.16 5 C 7386 2.51 5 N 1868 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11434 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5580 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 147 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5580 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 127 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.66, per 1000 atoms: 0.23 Number of scatterers: 11434 At special positions: 0 Unit cell: (104.64, 105.73, 139.52, 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 58 16.00 O 2122 8.00 N 1868 7.00 C 7386 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: 0.81 Conformation dependent library (CDL) restraints added in 529.2 milliseconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 64.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.501A pdb=" N LYS A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.751A pdb=" N VAL A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 203 through 252 removed outlier: 3.602A pdb=" N ALA A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.949A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 305 removed outlier: 4.428A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 4.641A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.592A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.680A pdb=" N GLU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.799A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.843A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 4.208A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.555A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.550A pdb=" N CYS A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.515A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 624 through 640 removed outlier: 3.814A pdb=" N ARG A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 removed outlier: 4.150A pdb=" N HIS A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 removed outlier: 4.337A pdb=" N ILE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.642A pdb=" N LYS A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.503A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 165 through 187 removed outlier: 3.788A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 203 through 252 removed outlier: 3.599A pdb=" N ALA B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.955A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 305 removed outlier: 4.566A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 4.654A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.611A pdb=" N GLY B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 417 removed outlier: 3.707A pdb=" N GLU B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 removed outlier: 3.819A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.805A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 445 through 464 removed outlier: 4.227A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 521 through 533 removed outlier: 3.560A pdb=" N ALA B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 575 through 581 removed outlier: 3.633A pdb=" N CYS B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.515A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.533A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 4.165A pdb=" N HIS B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 removed outlier: 4.343A pdb=" N ILE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.639A pdb=" N LYS B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 73 removed outlier: 4.297A pdb=" N GLY A 135 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.598A pdb=" N PHE A 488 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.589A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.664A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY B 135 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE B 92 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 133 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 11 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 506 through 509 removed outlier: 3.572A pdb=" N PHE B 488 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 565 removed outlier: 6.560A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2058 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: 2.24 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2319 1.34 - 1.46: 2394 1.46 - 1.58: 6793 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 11608 Sorted by residual: bond pdb=" N LYS A 328 " pdb=" CA LYS A 328 " ideal model delta sigma weight residual 1.463 1.493 -0.030 6.90e-03 2.10e+04 1.89e+01 bond pdb=" N LYS B 328 " pdb=" CA LYS B 328 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.78e+01 bond pdb=" N LYS B 163 " pdb=" CA LYS B 163 " ideal model delta sigma weight residual 1.462 1.493 -0.031 8.50e-03 1.38e+04 1.32e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.461 1.504 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" N ILE B 289 " pdb=" CA ILE B 289 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.09e-02 8.42e+03 1.31e+01 ... (remaining 11603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 9671 1.55 - 3.10: 4407 3.10 - 4.65: 1278 4.65 - 6.20: 281 6.20 - 7.75: 9 Bond angle restraints: 15646 Sorted by residual: angle pdb=" N ILE A 276 " pdb=" CA ILE A 276 " pdb=" CB ILE A 276 " ideal model delta sigma weight residual 110.55 116.75 -6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" C ALA B 159 " pdb=" N GLY B 160 " pdb=" CA GLY B 160 " ideal model delta sigma weight residual 120.03 125.68 -5.65 1.12e+00 7.97e-01 2.55e+01 angle pdb=" C ALA A 159 " pdb=" N GLY A 160 " pdb=" CA GLY A 160 " ideal model delta sigma weight residual 120.03 125.63 -5.60 1.12e+00 7.97e-01 2.50e+01 angle pdb=" C GLU A 625 " pdb=" N GLY A 626 " pdb=" CA GLY A 626 " ideal model delta sigma weight residual 120.03 125.51 -5.48 1.12e+00 7.97e-01 2.39e+01 angle pdb=" C GLY B 297 " pdb=" N GLY B 298 " pdb=" CA GLY B 298 " ideal model delta sigma weight residual 119.94 125.37 -5.43 1.11e+00 8.12e-01 2.39e+01 ... (remaining 15641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 6301 17.01 - 34.02: 539 34.02 - 51.04: 145 51.04 - 68.05: 31 68.05 - 85.06: 6 Dihedral angle restraints: 7022 sinusoidal: 2776 harmonic: 4246 Sorted by residual: dihedral pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N PRO A 86 " pdb=" CA PRO A 86 " ideal model delta harmonic sigma weight residual 0.00 28.41 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N THR A 133 " pdb=" CA THR A 133 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA TRP B 132 " pdb=" C TRP B 132 " pdb=" N THR B 133 " pdb=" CA THR B 133 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 629 0.048 - 0.096: 685 0.096 - 0.144: 406 0.144 - 0.192: 119 0.192 - 0.240: 13 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE B 486 " pdb=" N ILE B 486 " pdb=" C ILE B 486 " pdb=" CB ILE B 486 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE A 486 " pdb=" N ILE A 486 " pdb=" C ILE A 486 " pdb=" CB ILE A 486 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1849 not shown) Planarity restraints: 1950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 611 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C LYS A 611 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 611 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 612 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 94 " 0.006 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C ASP B 94 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 94 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 132 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C TRP B 132 " -0.022 2.00e-02 2.50e+03 pdb=" O TRP B 132 " 0.008 2.00e-02 2.50e+03 pdb=" N THR B 133 " 0.008 2.00e-02 2.50e+03 ... (remaining 1947 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2545 2.89 - 3.39: 12424 3.39 - 3.89: 18251 3.89 - 4.40: 19316 4.40 - 4.90: 34882 Nonbonded interactions: 87418 Sorted by model distance: nonbonded pdb=" O VAL A 11 " pdb=" OH TYR A 104 " model vdw 2.382 3.040 nonbonded pdb=" O VAL B 11 " pdb=" OH TYR B 104 " model vdw 2.393 3.040 nonbonded pdb=" O ALA A 98 " pdb=" CA GLY C 24 " model vdw 2.431 3.440 nonbonded pdb=" O LEU A 610 " pdb=" OG1 THR A 614 " model vdw 2.432 3.040 nonbonded pdb=" O LEU B 610 " pdb=" OG1 THR B 614 " model vdw 2.486 3.040 ... (remaining 87413 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' } 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: 2.370 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.014 0.045 11608 Z= 1.096 Angle : 1.878 7.751 15646 Z= 1.442 Chirality : 0.086 0.240 1852 Planarity : 0.003 0.019 1950 Dihedral : 14.269 85.061 4294 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.97 % Allowed : 9.73 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.18), residues: 1464 helix: -1.56 (0.14), residues: 864 sheet: -2.13 (0.41), residues: 118 loop : -2.12 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 559 TYR 0.018 0.002 TYR A 246 PHE 0.020 0.002 PHE B 67 TRP 0.019 0.003 TRP B 132 HIS 0.006 0.002 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.01396 (11608) covalent geometry : angle 1.87754 (15646) hydrogen bonds : bond 0.19424 ( 711) hydrogen bonds : angle 7.34024 ( 2058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8726 (ttm) cc_final: 0.8489 (ttt) REVERT: A 255 MET cc_start: 0.8441 (mmm) cc_final: 0.7880 (mmm) REVERT: A 278 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: A 288 MET cc_start: 0.8212 (mtp) cc_final: 0.7928 (mmp) REVERT: A 340 ASP cc_start: 0.8631 (m-30) cc_final: 0.8326 (m-30) REVERT: A 478 PHE cc_start: 0.8052 (m-80) cc_final: 0.7816 (m-80) REVERT: A 567 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6138 (tp40) REVERT: A 647 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7814 (t70) REVERT: C 18 LEU cc_start: 0.8777 (mt) cc_final: 0.8542 (mm) REVERT: C 19 MET cc_start: 0.8493 (ttm) cc_final: 0.8274 (tpp) REVERT: C 20 GLU cc_start: 0.8751 (tt0) cc_final: 0.8493 (tp30) REVERT: B 81 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8337 (ttpp) REVERT: B 154 MET cc_start: 0.8266 (mmm) cc_final: 0.7855 (mmt) REVERT: B 243 MET cc_start: 0.8702 (mtm) cc_final: 0.8442 (mtt) REVERT: B 290 ASP cc_start: 0.8950 (m-30) cc_final: 0.8673 (m-30) REVERT: B 420 MET cc_start: 0.8959 (ptp) cc_final: 0.8570 (ptm) REVERT: B 517 ILE cc_start: 0.9207 (mt) cc_final: 0.8988 (mm) REVERT: B 589 MET cc_start: 0.8039 (tmm) cc_final: 0.7739 (tmm) REVERT: B 647 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 37 outliers final: 16 residues processed: 167 average time/residue: 0.0993 time to fit residues: 24.3444 Evaluate side-chains 102 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 259 ASN A 278 GLN A 629 GLN A 704 HIS B 99 HIS B 259 ASN B 278 GLN B 567 GLN B 617 ASN B 704 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046389 restraints weight = 49090.719| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.18 r_work: 0.2812 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11608 Z= 0.128 Angle : 0.532 8.518 15646 Z= 0.286 Chirality : 0.039 0.147 1852 Planarity : 0.003 0.019 1950 Dihedral : 6.104 55.124 1600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.25 % Allowed : 13.34 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.81 (0.22), residues: 1464 helix: 1.82 (0.17), residues: 866 sheet: -0.97 (0.41), residues: 148 loop : -1.49 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.011 0.001 TYR A 225 PHE 0.014 0.001 PHE B 383 TRP 0.014 0.002 TRP A 132 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd covalent geometry : bond 0.00273 (11608) covalent geometry : angle 0.53173 (15646) hydrogen bonds : bond 0.04279 ( 711) hydrogen bonds : angle 4.31870 ( 2058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7978 (pp) REVERT: A 278 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: A 288 MET cc_start: 0.8588 (mtp) cc_final: 0.8102 (mmp) REVERT: A 589 MET cc_start: 0.8136 (mmm) cc_final: 0.7706 (mmm) REVERT: A 647 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8194 (t0) REVERT: B 154 MET cc_start: 0.8656 (mmm) cc_final: 0.8246 (mmt) REVERT: B 420 MET cc_start: 0.8823 (ptp) cc_final: 0.8441 (ptm) REVERT: B 517 ILE cc_start: 0.9605 (mt) cc_final: 0.9386 (mm) REVERT: B 647 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8443 (t0) REVERT: D 20 GLU cc_start: 0.8942 (tp30) cc_final: 0.8578 (tm-30) outliers start: 28 outliers final: 12 residues processed: 108 average time/residue: 0.0839 time to fit residues: 14.1408 Evaluate side-chains 87 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 127 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048969 restraints weight = 47282.959| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.04 r_work: 0.2920 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11608 Z= 0.182 Angle : 0.525 6.208 15646 Z= 0.281 Chirality : 0.040 0.161 1852 Planarity : 0.003 0.023 1950 Dihedral : 5.099 53.398 1582 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.89 % Allowed : 14.55 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.48 (0.22), residues: 1464 helix: 2.28 (0.18), residues: 872 sheet: -0.48 (0.43), residues: 142 loop : -1.19 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.010 0.001 TYR A 319 PHE 0.014 0.002 PHE B 257 TRP 0.008 0.002 TRP A 132 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00408 (11608) covalent geometry : angle 0.52541 (15646) hydrogen bonds : bond 0.04354 ( 711) hydrogen bonds : angle 4.21001 ( 2058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8806 (tpt) cc_final: 0.7873 (tmm) REVERT: A 271 MET cc_start: 0.8699 (tpp) cc_final: 0.8389 (tpp) REVERT: A 278 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: A 288 MET cc_start: 0.8719 (mtp) cc_final: 0.8246 (mmp) REVERT: A 293 MET cc_start: 0.8800 (ttt) cc_final: 0.8538 (mmp) REVERT: A 338 MET cc_start: 0.8728 (mmm) cc_final: 0.8479 (mmt) REVERT: A 598 MET cc_start: 0.9042 (mpp) cc_final: 0.8814 (mpp) REVERT: B 125 MET cc_start: 0.8317 (tpp) cc_final: 0.7203 (tmm) REVERT: B 154 MET cc_start: 0.8653 (mmm) cc_final: 0.8131 (mmt) REVERT: B 356 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: B 387 MET cc_start: 0.9306 (tpp) cc_final: 0.8997 (tpp) REVERT: B 420 MET cc_start: 0.8742 (ptp) cc_final: 0.8372 (ptm) REVERT: B 647 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8622 (t0) REVERT: D 20 GLU cc_start: 0.9044 (tp30) cc_final: 0.8683 (tm-30) outliers start: 36 outliers final: 13 residues processed: 102 average time/residue: 0.0760 time to fit residues: 12.6595 Evaluate side-chains 85 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 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 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053471 restraints weight = 44901.252| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.65 r_work: 0.3113 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11608 Z= 0.124 Angle : 0.471 6.352 15646 Z= 0.252 Chirality : 0.038 0.145 1852 Planarity : 0.002 0.019 1950 Dihedral : 4.593 51.772 1571 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.09 % Allowed : 15.76 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.82 (0.23), residues: 1464 helix: 2.50 (0.18), residues: 880 sheet: -0.29 (0.44), residues: 144 loop : -1.00 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.010 0.001 TYR A 225 PHE 0.014 0.001 PHE B 257 TRP 0.008 0.001 TRP B 132 HIS 0.005 0.001 HIS B 602 Details of bonding type rmsd covalent geometry : bond 0.00271 (11608) covalent geometry : angle 0.47108 (15646) hydrogen bonds : bond 0.03901 ( 711) hydrogen bonds : angle 3.90478 ( 2058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8694 (tpt) cc_final: 0.7856 (tmm) REVERT: A 278 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: A 288 MET cc_start: 0.8833 (mtp) cc_final: 0.8365 (mmp) REVERT: B 154 MET cc_start: 0.8756 (mmm) cc_final: 0.8207 (mmt) REVERT: B 420 MET cc_start: 0.8620 (ptp) cc_final: 0.8405 (ptm) REVERT: B 647 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8690 (t0) REVERT: D 20 GLU cc_start: 0.8889 (tp30) cc_final: 0.8546 (tm-30) outliers start: 26 outliers final: 13 residues processed: 94 average time/residue: 0.0806 time to fit residues: 12.3529 Evaluate side-chains 83 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 36 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 414 ASN B 305 ASN B 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053790 restraints weight = 44814.537| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.68 r_work: 0.3108 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11608 Z= 0.109 Angle : 0.456 7.711 15646 Z= 0.242 Chirality : 0.038 0.143 1852 Planarity : 0.002 0.026 1950 Dihedral : 4.417 48.442 1571 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.09 % Allowed : 15.59 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.05 (0.23), residues: 1464 helix: 2.62 (0.18), residues: 874 sheet: -0.16 (0.44), residues: 144 loop : -0.71 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 559 TYR 0.010 0.001 TYR A 225 PHE 0.019 0.001 PHE A 128 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00230 (11608) covalent geometry : angle 0.45574 (15646) hydrogen bonds : bond 0.03637 ( 711) hydrogen bonds : angle 3.71953 ( 2058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8704 (tpt) cc_final: 0.7844 (tmm) REVERT: A 255 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7402 (ttt) REVERT: A 278 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8608 (tm-30) REVERT: A 288 MET cc_start: 0.8879 (mtp) cc_final: 0.8404 (mmp) REVERT: A 338 MET cc_start: 0.8930 (mmm) cc_final: 0.8575 (mmt) REVERT: A 387 MET cc_start: 0.9342 (tpp) cc_final: 0.9003 (tpp) REVERT: C 17 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: B 125 MET cc_start: 0.8486 (tpp) cc_final: 0.7430 (tmm) REVERT: B 154 MET cc_start: 0.8813 (mmm) cc_final: 0.8179 (mmt) REVERT: B 305 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 420 MET cc_start: 0.8620 (ptp) cc_final: 0.8391 (ptm) REVERT: B 668 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9274 (mm) REVERT: D 20 GLU cc_start: 0.8858 (tp30) cc_final: 0.8550 (tm-30) outliers start: 26 outliers final: 10 residues processed: 96 average time/residue: 0.0726 time to fit residues: 11.4449 Evaluate side-chains 85 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 414 ASN B 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055785 restraints weight = 46562.872| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.60 r_work: 0.3090 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11608 Z= 0.105 Angle : 0.457 8.431 15646 Z= 0.240 Chirality : 0.038 0.142 1852 Planarity : 0.002 0.022 1950 Dihedral : 3.935 38.907 1565 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.16 (0.23), residues: 1464 helix: 2.67 (0.18), residues: 870 sheet: -0.10 (0.44), residues: 144 loop : -0.57 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.010 0.001 TYR A 225 PHE 0.015 0.001 PHE B 383 TRP 0.008 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00228 (11608) covalent geometry : angle 0.45656 (15646) hydrogen bonds : bond 0.03524 ( 711) hydrogen bonds : angle 3.65420 ( 2058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8613 (tpt) cc_final: 0.7982 (tmm) REVERT: A 154 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8101 (mtt) REVERT: A 271 MET cc_start: 0.8777 (tmm) cc_final: 0.8554 (tmm) REVERT: A 278 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: A 288 MET cc_start: 0.8877 (mtp) cc_final: 0.8424 (mmp) REVERT: A 387 MET cc_start: 0.9291 (tpp) cc_final: 0.8957 (tpp) REVERT: C 17 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: B 125 MET cc_start: 0.8533 (tpp) cc_final: 0.7478 (tmm) REVERT: B 197 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9328 (mm) REVERT: B 420 MET cc_start: 0.8613 (ptp) cc_final: 0.8404 (ptm) REVERT: B 668 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9270 (mm) REVERT: D 20 GLU cc_start: 0.8820 (tp30) cc_final: 0.8512 (tm-30) outliers start: 25 outliers final: 11 residues processed: 90 average time/residue: 0.0761 time to fit residues: 11.2442 Evaluate side-chains 86 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 414 ASN A 617 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.063651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.053563 restraints weight = 45146.039| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.85 r_work: 0.3087 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11608 Z= 0.092 Angle : 0.452 9.387 15646 Z= 0.234 Chirality : 0.038 0.141 1852 Planarity : 0.002 0.018 1950 Dihedral : 3.684 35.550 1563 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.01 % Allowed : 16.24 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.25 (0.23), residues: 1464 helix: 2.76 (0.18), residues: 856 sheet: 0.06 (0.44), residues: 140 loop : -0.50 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 472 TYR 0.010 0.001 TYR A 179 PHE 0.024 0.001 PHE A 128 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00188 (11608) covalent geometry : angle 0.45180 (15646) hydrogen bonds : bond 0.03316 ( 711) hydrogen bonds : angle 3.56705 ( 2058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8678 (tpt) cc_final: 0.8029 (tmm) REVERT: A 154 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: A 271 MET cc_start: 0.8777 (tmm) cc_final: 0.8530 (tmm) REVERT: A 288 MET cc_start: 0.8895 (mtp) cc_final: 0.8437 (mmp) REVERT: A 338 MET cc_start: 0.8854 (mmm) cc_final: 0.8507 (mmt) REVERT: A 387 MET cc_start: 0.9284 (tpp) cc_final: 0.8953 (tpp) REVERT: A 648 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6624 (tm-30) REVERT: B 125 MET cc_start: 0.8543 (tpp) cc_final: 0.7469 (tmm) REVERT: B 197 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9331 (mm) REVERT: B 420 MET cc_start: 0.8715 (ptp) cc_final: 0.8463 (ptm) REVERT: B 668 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9264 (mm) REVERT: D 20 GLU cc_start: 0.8836 (tp30) cc_final: 0.8619 (tm-30) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 0.0766 time to fit residues: 12.7532 Evaluate side-chains 88 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 305 ASN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.060252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050214 restraints weight = 45704.923| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.76 r_work: 0.2982 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11608 Z= 0.204 Angle : 0.543 9.696 15646 Z= 0.282 Chirality : 0.039 0.171 1852 Planarity : 0.002 0.017 1950 Dihedral : 3.793 16.264 1560 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.57 % Allowed : 16.56 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.22), residues: 1464 helix: 2.64 (0.18), residues: 850 sheet: -0.15 (0.44), residues: 144 loop : -0.48 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 109 TYR 0.012 0.001 TYR A 225 PHE 0.017 0.002 PHE A 428 TRP 0.011 0.002 TRP A 132 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00462 (11608) covalent geometry : angle 0.54312 (15646) hydrogen bonds : bond 0.04185 ( 711) hydrogen bonds : angle 3.97547 ( 2058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8808 (tpt) cc_final: 0.8112 (tmm) REVERT: A 255 MET cc_start: 0.8357 (tpp) cc_final: 0.8149 (tpt) REVERT: A 271 MET cc_start: 0.8847 (tmm) cc_final: 0.8556 (tmm) REVERT: A 338 MET cc_start: 0.8955 (mmm) cc_final: 0.8618 (mmt) REVERT: A 387 MET cc_start: 0.9351 (tpp) cc_final: 0.8983 (tpp) REVERT: B 125 MET cc_start: 0.8543 (tpp) cc_final: 0.7509 (tmm) REVERT: B 420 MET cc_start: 0.8738 (ptp) cc_final: 0.8486 (ptm) REVERT: B 668 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9282 (mm) REVERT: D 20 GLU cc_start: 0.8939 (tp30) cc_final: 0.8707 (tm-30) outliers start: 32 outliers final: 19 residues processed: 99 average time/residue: 0.0774 time to fit residues: 12.6257 Evaluate side-chains 89 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 113 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.055123 restraints weight = 46453.395| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.54 r_work: 0.3052 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11608 Z= 0.121 Angle : 0.498 9.995 15646 Z= 0.256 Chirality : 0.038 0.141 1852 Planarity : 0.002 0.016 1950 Dihedral : 3.699 18.840 1560 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 17.44 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1464 helix: 2.69 (0.18), residues: 852 sheet: 0.07 (0.44), residues: 140 loop : -0.47 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 43 TYR 0.010 0.001 TYR A 179 PHE 0.028 0.001 PHE A 128 TRP 0.010 0.001 TRP A 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00265 (11608) covalent geometry : angle 0.49836 (15646) hydrogen bonds : bond 0.03757 ( 711) hydrogen bonds : angle 3.76400 ( 2058) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8709 (tpt) cc_final: 0.8101 (tmm) REVERT: A 255 MET cc_start: 0.8133 (tpp) cc_final: 0.7872 (tpt) REVERT: A 338 MET cc_start: 0.8917 (mmm) cc_final: 0.8590 (mmt) REVERT: A 387 MET cc_start: 0.9265 (tpp) cc_final: 0.8984 (tpp) REVERT: A 648 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: C 15 ASP cc_start: 0.8994 (p0) cc_final: 0.8770 (p0) REVERT: B 668 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9253 (mm) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.0774 time to fit residues: 11.9522 Evaluate side-chains 88 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.067142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.055842 restraints weight = 46984.562| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.37 r_work: 0.3161 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11608 Z= 0.110 Angle : 0.496 13.733 15646 Z= 0.252 Chirality : 0.038 0.141 1852 Planarity : 0.002 0.020 1950 Dihedral : 3.609 17.372 1560 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.77 % Allowed : 17.85 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.17 (0.23), residues: 1464 helix: 2.66 (0.18), residues: 858 sheet: 0.08 (0.42), residues: 160 loop : -0.52 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.009 0.001 TYR A 179 PHE 0.022 0.001 PHE A 428 TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00238 (11608) covalent geometry : angle 0.49622 (15646) hydrogen bonds : bond 0.03555 ( 711) hydrogen bonds : angle 3.71147 ( 2058) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8589 (tpt) cc_final: 0.8070 (tmm) REVERT: A 255 MET cc_start: 0.7948 (tpp) cc_final: 0.7649 (tpt) REVERT: A 338 MET cc_start: 0.8917 (mmm) cc_final: 0.8615 (mmt) REVERT: A 387 MET cc_start: 0.9138 (tpp) cc_final: 0.8859 (tpp) REVERT: A 589 MET cc_start: 0.8180 (mmm) cc_final: 0.7847 (mmm) REVERT: A 648 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: C 13 LEU cc_start: 0.9198 (mt) cc_final: 0.8961 (mt) outliers start: 22 outliers final: 17 residues processed: 94 average time/residue: 0.0774 time to fit residues: 12.0227 Evaluate side-chains 90 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 570 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.067631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056035 restraints weight = 46623.848| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.57 r_work: 0.3071 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11608 Z= 0.110 Angle : 0.515 11.539 15646 Z= 0.258 Chirality : 0.038 0.141 1852 Planarity : 0.002 0.013 1950 Dihedral : 3.586 17.180 1560 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 17.52 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.18 (0.23), residues: 1464 helix: 2.66 (0.18), residues: 860 sheet: 0.12 (0.42), residues: 160 loop : -0.51 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.010 0.001 TYR B 56 PHE 0.030 0.001 PHE A 128 TRP 0.010 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00243 (11608) covalent geometry : angle 0.51463 (15646) hydrogen bonds : bond 0.03503 ( 711) hydrogen bonds : angle 3.71191 ( 2058) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.08 seconds wall clock time: 33 minutes 54.04 seconds (2034.04 seconds total)