Starting phenix.real_space_refine on Tue Jul 29 17:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v9z_21132/07_2025/6v9z_21132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v9z_21132/07_2025/6v9z_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_21132/07_2025/6v9z_21132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v9z_21132/07_2025/6v9z_21132.map" model { file = "/net/cci-nas-00/data/ceres_data/6v9z_21132/07_2025/6v9z_21132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v9z_21132/07_2025/6v9z_21132.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 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: 7.33, per 1000 atoms: 0.64 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: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.50 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: 3.69 Time building geometry restraints manager: 3.02 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: 0.010 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.460 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP B 132 HIS 0.006 0.002 HIS B 660 PHE 0.020 0.002 PHE B 67 TYR 0.018 0.002 TYR A 246 ARG 0.006 0.001 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.19424 ( 711) hydrogen bonds : angle 7.34024 ( 2058) covalent geometry : bond 0.01396 (11608) covalent geometry : angle 1.87754 (15646) *********************** 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 : 1.220 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: 0.6139 (tp40) REVERT: A 647 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7814 (t70) REVERT: C 18 LEU cc_start: 0.8776 (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: 0.2287 time to fit residues: 55.2581 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 : 1.342 ------------------------------------------------------------------------------- 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 122 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 567 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046365 restraints weight = 48729.698| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.17 r_work: 0.2820 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2226 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= 0.132 Angle : 0.528 8.639 15646 Z= 0.286 Chirality : 0.039 0.149 1852 Planarity : 0.003 0.021 1950 Dihedral : 6.091 55.309 1600 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1464 helix: 1.79 (0.17), residues: 866 sheet: -0.98 (0.41), residues: 148 loop : -1.50 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 132 HIS 0.003 0.001 HIS A 602 PHE 0.013 0.001 PHE B 383 TYR 0.011 0.001 TYR A 225 ARG 0.003 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 711) hydrogen bonds : angle 4.33861 ( 2058) covalent geometry : bond 0.00275 (11608) covalent geometry : angle 0.52844 (15646) *********************** 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 : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7991 (pp) REVERT: A 278 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: A 288 MET cc_start: 0.8583 (mtp) cc_final: 0.8103 (mmp) REVERT: A 589 MET cc_start: 0.8136 (mmm) cc_final: 0.7703 (mmm) REVERT: A 647 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8194 (t0) REVERT: B 154 MET cc_start: 0.8651 (mmm) cc_final: 0.8236 (mmt) REVERT: B 420 MET cc_start: 0.8842 (ptp) cc_final: 0.8500 (ptm) REVERT: B 517 ILE cc_start: 0.9608 (mt) cc_final: 0.9390 (mm) REVERT: B 647 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8156 (t0) REVERT: D 20 GLU cc_start: 0.8945 (tp30) cc_final: 0.8590 (tm-30) outliers start: 28 outliers final: 13 residues processed: 108 average time/residue: 0.1962 time to fit residues: 32.7233 Evaluate side-chains 90 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 218 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 112 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.059659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049399 restraints weight = 47236.375| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.11 r_work: 0.2932 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11608 Z= 0.166 Angle : 0.513 6.952 15646 Z= 0.275 Chirality : 0.039 0.161 1852 Planarity : 0.002 0.020 1950 Dihedral : 5.063 53.524 1582 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.73 % Allowed : 14.55 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1464 helix: 2.33 (0.18), residues: 872 sheet: -0.47 (0.43), residues: 142 loop : -1.14 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 132 HIS 0.003 0.001 HIS B 60 PHE 0.014 0.001 PHE B 257 TYR 0.010 0.001 TYR A 225 ARG 0.004 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 711) hydrogen bonds : angle 4.14544 ( 2058) covalent geometry : bond 0.00372 (11608) covalent geometry : angle 0.51292 (15646) *********************** 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 107 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8794 (tpt) cc_final: 0.7874 (tmm) REVERT: A 271 MET cc_start: 0.8693 (tpp) cc_final: 0.8390 (tpp) REVERT: A 278 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: A 288 MET cc_start: 0.8675 (mtp) cc_final: 0.8207 (mmp) REVERT: A 293 MET cc_start: 0.8812 (ttt) cc_final: 0.8539 (mmp) REVERT: A 338 MET cc_start: 0.8709 (mmm) cc_final: 0.8460 (mmt) REVERT: A 598 MET cc_start: 0.9083 (mpp) cc_final: 0.8783 (mpp) REVERT: B 125 MET cc_start: 0.8300 (tpp) cc_final: 0.7167 (tmm) REVERT: B 154 MET cc_start: 0.8589 (mmm) cc_final: 0.8100 (mmt) REVERT: B 420 MET cc_start: 0.8746 (ptp) cc_final: 0.8373 (ptm) REVERT: B 467 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9042 (t) REVERT: B 647 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8646 (t0) REVERT: D 20 GLU cc_start: 0.9034 (tp30) cc_final: 0.8658 (tm-30) outliers start: 34 outliers final: 14 residues processed: 103 average time/residue: 0.1808 time to fit residues: 30.0095 Evaluate side-chains 82 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 218 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 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 218 LEU Chi-restraints excluded: chain B residue 467 THR 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 44 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.063201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.053280 restraints weight = 44605.640| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.63 r_work: 0.3070 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11608 Z= 0.138 Angle : 0.477 6.583 15646 Z= 0.255 Chirality : 0.039 0.144 1852 Planarity : 0.002 0.020 1950 Dihedral : 4.627 51.755 1573 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.25 % Allowed : 16.08 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1464 helix: 2.56 (0.18), residues: 872 sheet: -0.20 (0.44), residues: 140 loop : -0.96 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.005 0.001 HIS B 602 PHE 0.014 0.001 PHE B 257 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 711) hydrogen bonds : angle 3.91950 ( 2058) covalent geometry : bond 0.00306 (11608) covalent geometry : angle 0.47712 (15646) *********************** 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: 28 poor density : 71 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8703 (tpt) cc_final: 0.7857 (tmm) REVERT: A 278 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: A 288 MET cc_start: 0.8842 (mtp) cc_final: 0.8365 (mmp) REVERT: A 598 MET cc_start: 0.9025 (mpp) cc_final: 0.8792 (mpp) REVERT: B 154 MET cc_start: 0.8751 (mmm) cc_final: 0.8208 (mmt) REVERT: B 387 MET cc_start: 0.9300 (tpp) cc_final: 0.9091 (tpp) REVERT: B 420 MET cc_start: 0.8630 (ptp) cc_final: 0.8391 (ptm) REVERT: B 647 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8697 (t70) REVERT: D 20 GLU cc_start: 0.8891 (tp30) cc_final: 0.8532 (tm-30) outliers start: 28 outliers final: 13 residues processed: 95 average time/residue: 0.1795 time to fit residues: 27.7256 Evaluate side-chains 81 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 218 LEU 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 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 99 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.063961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053990 restraints weight = 44282.088| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.70 r_work: 0.3196 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3229 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= 0.099 Angle : 0.449 7.920 15646 Z= 0.237 Chirality : 0.038 0.144 1852 Planarity : 0.002 0.018 1950 Dihedral : 4.362 47.727 1571 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 16.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.23), residues: 1464 helix: 2.67 (0.18), residues: 874 sheet: -0.11 (0.44), residues: 144 loop : -0.73 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.002 0.001 HIS B 602 PHE 0.013 0.001 PHE B 257 TYR 0.009 0.001 TYR A 225 ARG 0.001 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 711) hydrogen bonds : angle 3.66603 ( 2058) covalent geometry : bond 0.00207 (11608) covalent geometry : angle 0.44868 (15646) *********************** 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 99 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8580 (tpt) cc_final: 0.7988 (tmm) REVERT: A 255 MET cc_start: 0.8484 (mmm) cc_final: 0.8034 (mmm) REVERT: A 278 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8722 (tm-30) REVERT: A 288 MET cc_start: 0.8802 (mtp) cc_final: 0.8347 (mmm) REVERT: A 338 MET cc_start: 0.8941 (mmm) cc_final: 0.8587 (mmt) REVERT: A 387 MET cc_start: 0.9249 (tpp) cc_final: 0.8933 (tpp) REVERT: A 589 MET cc_start: 0.8195 (mmm) cc_final: 0.7794 (mmm) REVERT: A 598 MET cc_start: 0.8923 (mpp) cc_final: 0.8705 (mpp) REVERT: B 125 MET cc_start: 0.8502 (tpp) cc_final: 0.7521 (tmm) REVERT: B 154 MET cc_start: 0.8819 (mmm) cc_final: 0.8164 (mmt) REVERT: B 305 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7121 (t0) REVERT: D 20 GLU cc_start: 0.8706 (tp30) cc_final: 0.8433 (tm-30) outliers start: 22 outliers final: 5 residues processed: 94 average time/residue: 0.1900 time to fit residues: 28.5310 Evaluate side-chains 73 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 543 ILE 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 305 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 652 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053003 restraints weight = 45393.794| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.85 r_work: 0.3065 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3363 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= 0.101 Angle : 0.455 8.428 15646 Z= 0.239 Chirality : 0.038 0.142 1852 Planarity : 0.002 0.015 1950 Dihedral : 3.764 37.901 1563 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.77 % Allowed : 16.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.23), residues: 1464 helix: 2.76 (0.18), residues: 860 sheet: -0.02 (0.44), residues: 144 loop : -0.57 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.020 0.001 PHE A 128 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 711) hydrogen bonds : angle 3.64466 ( 2058) covalent geometry : bond 0.00215 (11608) covalent geometry : angle 0.45513 (15646) *********************** 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 93 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8658 (tpt) cc_final: 0.8009 (tmm) REVERT: A 278 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: A 288 MET cc_start: 0.8897 (mtp) cc_final: 0.8415 (mmp) REVERT: A 387 MET cc_start: 0.9310 (tpp) cc_final: 0.8965 (tpp) REVERT: A 598 MET cc_start: 0.9015 (mpp) cc_final: 0.8678 (mpp) REVERT: C 15 ASP cc_start: 0.9002 (p0) cc_final: 0.8775 (p0) REVERT: B 125 MET cc_start: 0.8517 (tpp) cc_final: 0.7443 (tmm) REVERT: D 20 GLU cc_start: 0.8839 (tp30) cc_final: 0.8524 (tm-30) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 0.1819 time to fit residues: 26.3098 Evaluate side-chains 79 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 239 ASP 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 18 LEU Chi-restraints excluded: chain B residue 570 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.067619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055946 restraints weight = 47016.342| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.58 r_work: 0.3068 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3500 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= 0.111 Angle : 0.471 9.264 15646 Z= 0.242 Chirality : 0.039 0.270 1852 Planarity : 0.002 0.018 1950 Dihedral : 3.733 38.189 1563 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.93 % Allowed : 16.80 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.23), residues: 1464 helix: 2.74 (0.18), residues: 860 sheet: -0.05 (0.44), residues: 144 loop : -0.49 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.019 0.001 PHE A 428 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 711) hydrogen bonds : angle 3.65889 ( 2058) covalent geometry : bond 0.00240 (11608) covalent geometry : angle 0.47116 (15646) *********************** 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 99 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8645 (tpt) cc_final: 0.8014 (tmm) REVERT: A 255 MET cc_start: 0.8567 (mmm) cc_final: 0.8163 (mmm) REVERT: A 278 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: A 288 MET cc_start: 0.8887 (mtp) cc_final: 0.8454 (mmp) REVERT: A 338 MET cc_start: 0.8869 (mmm) cc_final: 0.8527 (mmt) REVERT: A 387 MET cc_start: 0.9277 (tpp) cc_final: 0.8949 (tpp) REVERT: A 589 MET cc_start: 0.8148 (mmm) cc_final: 0.7855 (mmm) REVERT: A 598 MET cc_start: 0.9001 (mpp) cc_final: 0.8765 (mpp) REVERT: A 648 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 125 MET cc_start: 0.8540 (tpp) cc_final: 0.7492 (tmm) REVERT: B 197 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9328 (mm) REVERT: D 15 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7997 (t70) REVERT: D 20 GLU cc_start: 0.8784 (tp30) cc_final: 0.8548 (tm-30) outliers start: 24 outliers final: 9 residues processed: 95 average time/residue: 0.1824 time to fit residues: 27.9378 Evaluate side-chains 80 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 239 ASP 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 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 B 660 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.058440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048407 restraints weight = 46964.293| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.75 r_work: 0.2938 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 11608 Z= 0.310 Angle : 0.655 9.229 15646 Z= 0.339 Chirality : 0.042 0.351 1852 Planarity : 0.003 0.021 1950 Dihedral : 4.307 51.663 1563 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.73 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.22), residues: 1464 helix: 2.38 (0.18), residues: 850 sheet: 0.02 (0.45), residues: 140 loop : -0.62 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 132 HIS 0.007 0.001 HIS B 249 PHE 0.018 0.002 PHE B 257 TYR 0.013 0.002 TYR A 319 ARG 0.003 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 711) hydrogen bonds : angle 4.37043 ( 2058) covalent geometry : bond 0.00696 (11608) covalent geometry : angle 0.65473 (15646) *********************** 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 100 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8896 (tpt) cc_final: 0.8206 (tmm) REVERT: A 255 MET cc_start: 0.8739 (mmm) cc_final: 0.8125 (mmm) REVERT: A 271 MET cc_start: 0.8821 (tpp) cc_final: 0.8455 (tmm) REVERT: A 278 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: A 338 MET cc_start: 0.8948 (mmm) cc_final: 0.8615 (mmt) REVERT: A 387 MET cc_start: 0.9389 (tpp) cc_final: 0.9069 (tpp) REVERT: A 570 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6405 (t80) REVERT: A 598 MET cc_start: 0.9102 (mpp) cc_final: 0.8708 (mpp) REVERT: B 125 MET cc_start: 0.8545 (tpp) cc_final: 0.7568 (tmm) REVERT: B 612 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7951 (m-10) REVERT: D 15 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8182 (t70) REVERT: D 20 GLU cc_start: 0.8907 (tp30) cc_final: 0.8605 (tm-30) outliers start: 34 outliers final: 21 residues processed: 97 average time/residue: 0.1840 time to fit residues: 28.8383 Evaluate side-chains 85 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 239 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 278 GLN 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 570 PHE Chi-restraints excluded: chain A residue 605 ILE 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 337 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 612 TYR Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.066421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.054606 restraints weight = 47134.120| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.61 r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11608 Z= 0.126 Angle : 0.512 9.655 15646 Z= 0.265 Chirality : 0.039 0.245 1852 Planarity : 0.002 0.017 1950 Dihedral : 4.033 44.279 1563 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.85 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1464 helix: 2.63 (0.18), residues: 854 sheet: 0.20 (0.45), residues: 136 loop : -0.62 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS B 249 PHE 0.020 0.001 PHE B 383 TYR 0.010 0.001 TYR A 179 ARG 0.002 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 711) hydrogen bonds : angle 3.90653 ( 2058) covalent geometry : bond 0.00275 (11608) covalent geometry : angle 0.51247 (15646) *********************** 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 93 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8738 (tpt) cc_final: 0.8155 (tmm) REVERT: A 255 MET cc_start: 0.8615 (mmm) cc_final: 0.7987 (mmm) REVERT: A 271 MET cc_start: 0.8776 (tpp) cc_final: 0.8381 (tmm) REVERT: A 278 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8586 (tm-30) REVERT: A 338 MET cc_start: 0.8914 (mmm) cc_final: 0.8588 (mmt) REVERT: A 387 MET cc_start: 0.9313 (tpp) cc_final: 0.9029 (tpp) REVERT: A 570 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6188 (t80) REVERT: A 598 MET cc_start: 0.9097 (mpp) cc_final: 0.8760 (mpp) REVERT: D 15 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7992 (t70) REVERT: D 20 GLU cc_start: 0.8886 (tp30) cc_final: 0.8542 (tm-30) outliers start: 23 outliers final: 10 residues processed: 87 average time/residue: 0.1777 time to fit residues: 25.2163 Evaluate side-chains 77 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 278 GLN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 605 ILE 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 D residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 39 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 B 305 ASN B 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.052127 restraints weight = 45897.526| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.84 r_work: 0.3048 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11608 Z= 0.104 Angle : 0.497 10.321 15646 Z= 0.254 Chirality : 0.039 0.207 1852 Planarity : 0.002 0.022 1950 Dihedral : 3.862 40.417 1563 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.29 % Allowed : 18.41 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.23), residues: 1464 helix: 2.71 (0.18), residues: 856 sheet: 0.04 (0.42), residues: 160 loop : -0.57 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.030 0.001 PHE A 128 TYR 0.010 0.001 TYR B 179 ARG 0.001 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 711) hydrogen bonds : angle 3.74778 ( 2058) covalent geometry : bond 0.00223 (11608) covalent geometry : angle 0.49654 (15646) ********************** 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 88 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8728 (tpt) cc_final: 0.8088 (tmm) REVERT: A 255 MET cc_start: 0.8601 (mmm) cc_final: 0.6760 (mmm) REVERT: A 271 MET cc_start: 0.8817 (tpp) cc_final: 0.8446 (tmm) REVERT: A 278 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: A 338 MET cc_start: 0.8929 (mmm) cc_final: 0.8600 (mmt) REVERT: A 387 MET cc_start: 0.9302 (tpp) cc_final: 0.8988 (tpp) REVERT: A 570 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.6061 (t80) REVERT: A 598 MET cc_start: 0.9086 (mpp) cc_final: 0.8737 (mpp) REVERT: D 15 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8025 (t70) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.1804 time to fit residues: 24.7651 Evaluate side-chains 80 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 605 ILE 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 479 VAL Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 26 optimal weight: 0.6980 chunk 116 optimal weight: 0.0060 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.062611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052583 restraints weight = 45864.560| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.85 r_work: 0.3062 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11608 Z= 0.103 Angle : 0.500 13.970 15646 Z= 0.252 Chirality : 0.039 0.190 1852 Planarity : 0.002 0.021 1950 Dihedral : 3.796 38.751 1563 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.69 % Allowed : 18.01 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.23), residues: 1464 helix: 2.69 (0.18), residues: 860 sheet: 0.09 (0.42), residues: 160 loop : -0.55 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.021 0.001 PHE A 128 TYR 0.010 0.001 TYR A 179 ARG 0.001 0.000 ARG A 559 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 711) hydrogen bonds : angle 3.71075 ( 2058) covalent geometry : bond 0.00221 (11608) covalent geometry : angle 0.49983 (15646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6370.09 seconds wall clock time: 113 minutes 12.74 seconds (6792.74 seconds total)