Starting phenix.real_space_refine on Thu Jun 12 02:44:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923.map" model { file = "/net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho9_34923/06_2025/8ho9_34923_neut.cif" } resolution = 2.25 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= 0.000 sd= 1.000 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 32 5.16 5 C 8402 2.51 5 N 2190 2.21 5 O 2839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13463 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "B" Number of atoms: 6558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6558 Classifications: {'peptide': 811} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 781} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Time building chain proxies: 9.54, per 1000 atoms: 0.71 Number of scatterers: 13463 At special positions: 0 Unit cell: (133.63, 102.09, 97.94, 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 32 16.00 O 2839 8.00 N 2190 7.00 C 8402 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: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 26 sheets defined 33.7% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.821A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 344 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.616A pdb=" N LEU A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.678A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.928A pdb=" N TRP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.725A pdb=" N ILE A 437 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.939A pdb=" N VAL A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.079A pdb=" N LYS A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 557 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.608A pdb=" N GLY A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.411A pdb=" N ILE A 638 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 641 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.828A pdb=" N TRP A 658 " --> pdb=" O HIS A 654 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 680 removed outlier: 3.898A pdb=" N ILE A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 686 removed outlier: 3.734A pdb=" N GLU A 685 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP A 686 " --> pdb=" O TYR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.918A pdb=" N TRP A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.871A pdb=" N PHE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 314 Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 344 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.619A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.686A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 3.916A pdb=" N TRP B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.670A pdb=" N ILE B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.943A pdb=" N VAL B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.016A pdb=" N LYS B 524 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 586 through 595 removed outlier: 3.609A pdb=" N GLY B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 615 Processing helix chain 'B' and resid 635 through 641 removed outlier: 4.378A pdb=" N ILE B 638 " --> pdb=" O TYR B 635 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 641 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.823A pdb=" N TRP B 658 " --> pdb=" O HIS B 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.968A pdb=" N ILE B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 removed outlier: 3.710A pdb=" N GLU B 685 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP B 686 " --> pdb=" O TYR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 720 through 732 removed outlier: 3.803A pdb=" N TRP B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.681A pdb=" N SER A 95 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.479A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.479A pdb=" N ILE A 56 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 208 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER A 244 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 206 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.897A pdb=" N VAL A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 444 removed outlier: 4.151A pdb=" N PHE A 444 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS A 450 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AB2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.728A pdb=" N ALA A 699 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 716 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.916A pdb=" N LEU A 743 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 3.675A pdb=" N SER B 95 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.459A pdb=" N ILE B 56 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.459A pdb=" N ILE B 56 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 245 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 208 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 244 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 206 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.909A pdb=" N VAL B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 316 through 319 removed outlier: 6.598A pdb=" N THR B 766 " --> pdb=" O HIS B 805 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 807 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU B 768 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL B 809 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR B 770 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET B 811 " --> pdb=" O THR B 770 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS B 772 " --> pdb=" O MET B 811 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 358 through 359 Processing sheet with id=AC3, first strand: chain 'B' and resid 441 through 444 removed outlier: 4.145A pdb=" N PHE B 444 " --> pdb=" O LYS B 450 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS B 450 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC5, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=AC6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.688A pdb=" N ALA B 699 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER B 716 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 736 through 739 removed outlier: 3.963A pdb=" N LEU B 743 " --> pdb=" O LEU B 796 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1605 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: 5.86 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 0.96: 4 0.96 - 1.17: 0 1.17 - 1.39: 5586 1.39 - 1.60: 7808 1.60 - 1.81: 64 Bond restraints: 13462 Sorted by residual: bond pdb=" C LYS B 3 " pdb=" O LYS B 3 " ideal model delta sigma weight residual 1.235 0.746 0.489 1.28e-02 6.10e+03 1.46e+03 bond pdb=" C LYS A 3 " pdb=" O LYS A 3 " ideal model delta sigma weight residual 1.235 0.746 0.489 1.28e-02 6.10e+03 1.46e+03 bond pdb=" C GLY A 2 " pdb=" O GLY A 2 " ideal model delta sigma weight residual 1.231 0.870 0.361 2.00e-02 2.50e+03 3.26e+02 bond pdb=" C GLY B 2 " pdb=" O GLY B 2 " ideal model delta sigma weight residual 1.231 0.870 0.361 2.00e-02 2.50e+03 3.26e+02 bond pdb=" CA GLY B 2 " pdb=" C GLY B 2 " ideal model delta sigma weight residual 1.516 1.298 0.218 1.80e-02 3.09e+03 1.47e+02 ... (remaining 13457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 18167 4.10 - 8.20: 23 8.20 - 12.29: 12 12.29 - 16.39: 0 16.39 - 20.49: 4 Bond angle restraints: 18206 Sorted by residual: angle pdb=" C LYS B 3 " pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " ideal model delta sigma weight residual 109.37 129.86 -20.49 1.91e+00 2.74e-01 1.15e+02 angle pdb=" C LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta sigma weight residual 109.37 129.84 -20.47 1.91e+00 2.74e-01 1.15e+02 angle pdb=" CA GLY B 2 " pdb=" C GLY B 2 " pdb=" O GLY B 2 " ideal model delta sigma weight residual 120.80 103.91 16.89 2.10e+00 2.27e-01 6.47e+01 angle pdb=" CA GLY A 2 " pdb=" C GLY A 2 " pdb=" O GLY A 2 " ideal model delta sigma weight residual 120.80 103.97 16.83 2.10e+00 2.27e-01 6.42e+01 angle pdb=" N PHE A 4 " pdb=" CA PHE A 4 " pdb=" C PHE A 4 " ideal model delta sigma weight residual 112.30 101.99 10.31 1.36e+00 5.41e-01 5.74e+01 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6833 17.68 - 35.36: 761 35.36 - 53.05: 217 53.05 - 70.73: 51 70.73 - 88.41: 30 Dihedral angle restraints: 7892 sinusoidal: 3192 harmonic: 4700 Sorted by residual: dihedral pdb=" C LYS A 3 " pdb=" N LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta harmonic sigma weight residual -122.60 -147.11 24.51 0 2.50e+00 1.60e-01 9.61e+01 dihedral pdb=" C LYS B 3 " pdb=" N LYS B 3 " pdb=" CA LYS B 3 " pdb=" CB LYS B 3 " ideal model delta harmonic sigma weight residual -122.60 -147.09 24.49 0 2.50e+00 1.60e-01 9.60e+01 dihedral pdb=" N LYS A 3 " pdb=" C LYS A 3 " pdb=" CA LYS A 3 " pdb=" CB LYS A 3 " ideal model delta harmonic sigma weight residual 122.80 137.19 -14.39 0 2.50e+00 1.60e-01 3.31e+01 ... (remaining 7889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 1854 0.276 - 0.551: 1 0.551 - 0.827: 0 0.827 - 1.103: 2 1.103 - 1.378: 1 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CB THR B 503 " pdb=" CA THR B 503 " pdb=" OG1 THR B 503 " pdb=" CG2 THR B 503 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CA LYS B 3 " pdb=" N LYS B 3 " pdb=" C LYS B 3 " pdb=" CB LYS B 3 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA LYS A 3 " pdb=" N LYS A 3 " pdb=" C LYS A 3 " pdb=" CB LYS A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 1855 not shown) Planarity restraints: 2372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 2 " 0.014 2.00e-02 2.50e+03 3.09e-02 9.55e+00 pdb=" C GLY B 2 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B 2 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 3 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 2 " -0.014 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLY A 2 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 2 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 3 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 680 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 681 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 681 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 681 " 0.026 5.00e-02 4.00e+02 ... (remaining 2369 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 141 2.54 - 3.13: 10153 3.13 - 3.72: 22474 3.72 - 4.31: 36713 4.31 - 4.90: 54759 Nonbonded interactions: 124240 Sorted by model distance: nonbonded pdb=" O SER B 498 " pdb=" OG1 THR B 502 " model vdw 1.947 3.040 nonbonded pdb=" OG1 THR B 31 " pdb=" OE1 GLU B 32 " model vdw 1.963 3.040 nonbonded pdb=" O LEU A 693 " pdb=" O HOH A 901 " model vdw 2.003 3.040 nonbonded pdb=" O LEU B 693 " pdb=" O HOH B 901 " model vdw 2.005 3.040 nonbonded pdb=" O LEU B 124 " pdb=" O HOH B 902 " model vdw 2.008 3.040 ... (remaining 124235 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: 0.07 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: 5.590 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.380 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.009 0.489 13462 Z= 0.562 Angle : 0.692 20.488 18206 Z= 0.387 Chirality : 0.064 1.378 1858 Planarity : 0.004 0.046 2372 Dihedral : 17.346 88.410 4916 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.23 % Allowed : 14.96 % Favored : 83.82 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.34 % 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: 0.41 (0.21), residues: 1618 helix: 0.96 (0.24), residues: 482 sheet: 0.86 (0.29), residues: 294 loop : -0.29 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 245 PHE 0.014 0.002 PHE B 360 TYR 0.016 0.002 TYR A 14 ARG 0.006 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.12048 ( 572) hydrogen bonds : angle 6.42635 ( 1605) covalent geometry : bond 0.00859 (13462) covalent geometry : angle 0.69217 (18206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.487 Fit side-chains REVERT: A 91 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7979 (mtt180) REVERT: A 142 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7787 (tttm) REVERT: A 540 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6821 (mtm-85) REVERT: A 544 GLN cc_start: 0.7904 (mt0) cc_final: 0.7637 (mt0) outliers start: 17 outliers final: 14 residues processed: 147 average time/residue: 1.6645 time to fit residues: 262.7731 Evaluate side-chains 143 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099835 restraints weight = 13495.449| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.20 r_work: 0.3135 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13462 Z= 0.261 Angle : 0.686 7.627 18206 Z= 0.384 Chirality : 0.052 0.153 1858 Planarity : 0.006 0.054 2372 Dihedral : 7.076 56.649 1819 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.40 % Allowed : 12.50 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.15 (0.21), residues: 1618 helix: 0.54 (0.23), residues: 498 sheet: 0.92 (0.29), residues: 304 loop : -0.44 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 332 HIS 0.007 0.002 HIS A 245 PHE 0.019 0.003 PHE A 370 TYR 0.022 0.003 TYR A 463 ARG 0.004 0.001 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.06361 ( 572) hydrogen bonds : angle 5.99391 ( 1605) covalent geometry : bond 0.00600 (13462) covalent geometry : angle 0.68586 (18206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.677 Fit side-chains REVERT: A 258 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: A 275 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: A 315 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.7826 (mmtp) REVERT: A 536 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: A 544 GLN cc_start: 0.8424 (mt0) cc_final: 0.8186 (mt0) REVERT: B 258 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: B 272 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: B 275 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: B 290 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: B 538 GLU cc_start: 0.7790 (mp0) cc_final: 0.7499 (mp0) REVERT: B 561 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8154 (mm-30) outliers start: 47 outliers final: 23 residues processed: 166 average time/residue: 1.6554 time to fit residues: 296.2740 Evaluate side-chains 161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104384 restraints weight = 13553.916| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.22 r_work: 0.3206 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13462 Z= 0.115 Angle : 0.522 6.422 18206 Z= 0.293 Chirality : 0.045 0.142 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.899 55.564 1804 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.95 % Allowed : 13.58 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.49 (0.21), residues: 1618 helix: 0.97 (0.24), residues: 490 sheet: 1.04 (0.29), residues: 294 loop : -0.27 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS A 245 PHE 0.019 0.001 PHE A 370 TYR 0.014 0.001 TYR B 14 ARG 0.003 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 572) hydrogen bonds : angle 5.57522 ( 1605) covalent geometry : bond 0.00238 (13462) covalent geometry : angle 0.52158 (18206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.583 Fit side-chains REVERT: A 142 LYS cc_start: 0.8244 (mtpp) cc_final: 0.8009 (tttm) REVERT: A 540 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: B 142 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8154 (tttp) REVERT: B 258 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 538 GLU cc_start: 0.7726 (mp0) cc_final: 0.7514 (mp0) outliers start: 27 outliers final: 14 residues processed: 155 average time/residue: 1.7052 time to fit residues: 284.9506 Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100231 restraints weight = 13419.396| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.20 r_work: 0.3141 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13462 Z= 0.239 Angle : 0.654 7.759 18206 Z= 0.366 Chirality : 0.051 0.150 1858 Planarity : 0.005 0.052 2372 Dihedral : 6.182 52.918 1800 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.67 % Allowed : 13.37 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.35 (0.21), residues: 1618 helix: 0.77 (0.24), residues: 486 sheet: 1.04 (0.29), residues: 296 loop : -0.33 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.003 PHE A 370 TYR 0.021 0.002 TYR A 14 ARG 0.006 0.001 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.06014 ( 572) hydrogen bonds : angle 5.87180 ( 1605) covalent geometry : bond 0.00549 (13462) covalent geometry : angle 0.65351 (18206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.515 Fit side-chains REVERT: A 142 LYS cc_start: 0.8291 (mtpp) cc_final: 0.8045 (tttm) REVERT: A 258 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: A 275 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: A 290 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8488 (tm-30) REVERT: A 315 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.7832 (mmtp) REVERT: B 91 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8221 (mtt180) REVERT: B 258 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: B 275 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: B 290 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: B 538 GLU cc_start: 0.7805 (mp0) cc_final: 0.7484 (mp0) REVERT: B 561 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8168 (mm-30) outliers start: 37 outliers final: 18 residues processed: 162 average time/residue: 1.8095 time to fit residues: 316.5752 Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 0.0000 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 90 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 413 ASN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104408 restraints weight = 13479.303| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.21 r_work: 0.3203 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13462 Z= 0.112 Angle : 0.518 6.440 18206 Z= 0.291 Chirality : 0.045 0.143 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.571 46.805 1800 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.52 % Allowed : 14.60 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.50 (0.21), residues: 1618 helix: 1.02 (0.24), residues: 488 sheet: 1.06 (0.29), residues: 294 loop : -0.29 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.001 PHE A 370 TYR 0.014 0.001 TYR B 14 ARG 0.007 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 572) hydrogen bonds : angle 5.53234 ( 1605) covalent geometry : bond 0.00236 (13462) covalent geometry : angle 0.51763 (18206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 2.084 Fit side-chains REVERT: A 142 LYS cc_start: 0.8231 (mtpp) cc_final: 0.8021 (tttm) REVERT: A 258 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: B 91 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8174 (mtt180) REVERT: B 144 LYS cc_start: 0.8631 (tptp) cc_final: 0.8422 (tmtt) REVERT: B 258 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: B 538 GLU cc_start: 0.7756 (mp0) cc_final: 0.7511 (mp0) outliers start: 21 outliers final: 14 residues processed: 155 average time/residue: 2.2426 time to fit residues: 375.5407 Evaluate side-chains 149 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102573 restraints weight = 13624.007| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.22 r_work: 0.3174 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13462 Z= 0.153 Angle : 0.559 6.967 18206 Z= 0.314 Chirality : 0.047 0.150 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.570 45.105 1798 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.17 % Allowed : 14.23 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.58 (0.21), residues: 1618 helix: 1.11 (0.24), residues: 484 sheet: 1.04 (0.29), residues: 296 loop : -0.23 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE A 370 TYR 0.018 0.002 TYR B 14 ARG 0.008 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 572) hydrogen bonds : angle 5.60898 ( 1605) covalent geometry : bond 0.00338 (13462) covalent geometry : angle 0.55877 (18206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 2.802 Fit side-chains REVERT: A 142 LYS cc_start: 0.8219 (mtpp) cc_final: 0.8018 (tttm) REVERT: A 258 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: A 275 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: A 354 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7602 (mp) REVERT: B 91 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8192 (mtt180) REVERT: B 144 LYS cc_start: 0.8642 (tptp) cc_final: 0.8418 (tmtt) REVERT: B 258 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: B 272 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: B 538 GLU cc_start: 0.7804 (mp0) cc_final: 0.7530 (mp0) REVERT: B 561 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8150 (mm-30) outliers start: 30 outliers final: 17 residues processed: 157 average time/residue: 2.6840 time to fit residues: 455.0526 Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 792 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105488 restraints weight = 13556.853| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.22 r_work: 0.3216 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13462 Z= 0.105 Angle : 0.500 6.299 18206 Z= 0.280 Chirality : 0.044 0.143 1858 Planarity : 0.004 0.040 2372 Dihedral : 5.128 45.422 1798 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.81 % Allowed : 14.74 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.66 (0.21), residues: 1618 helix: 1.26 (0.24), residues: 486 sheet: 1.04 (0.29), residues: 294 loop : -0.22 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.004 0.001 HIS B 245 PHE 0.018 0.001 PHE A 370 TYR 0.013 0.001 TYR B 14 ARG 0.008 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 572) hydrogen bonds : angle 5.41377 ( 1605) covalent geometry : bond 0.00219 (13462) covalent geometry : angle 0.49967 (18206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 2.073 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: A 354 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7600 (mp) REVERT: A 538 GLU cc_start: 0.7854 (mp0) cc_final: 0.7550 (mp0) REVERT: B 91 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8132 (mtt180) REVERT: B 144 LYS cc_start: 0.8637 (tptp) cc_final: 0.8405 (tmtt) REVERT: B 258 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 538 GLU cc_start: 0.7792 (mp0) cc_final: 0.7538 (mp0) REVERT: B 561 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8114 (mm-30) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 2.0851 time to fit residues: 352.8102 Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN A 805 HIS B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102988 restraints weight = 13503.609| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.21 r_work: 0.3182 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13462 Z= 0.149 Angle : 0.552 6.935 18206 Z= 0.310 Chirality : 0.046 0.150 1858 Planarity : 0.004 0.039 2372 Dihedral : 5.246 45.733 1795 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.73 % Allowed : 14.52 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.61 (0.21), residues: 1618 helix: 1.15 (0.24), residues: 484 sheet: 1.07 (0.29), residues: 294 loop : -0.23 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE B 370 TYR 0.018 0.002 TYR B 14 ARG 0.008 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 572) hydrogen bonds : angle 5.56165 ( 1605) covalent geometry : bond 0.00331 (13462) covalent geometry : angle 0.55245 (18206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: A 538 GLU cc_start: 0.7948 (mp0) cc_final: 0.7602 (mp0) REVERT: B 91 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8170 (mtt180) REVERT: B 144 LYS cc_start: 0.8633 (tptp) cc_final: 0.8390 (tmtt) REVERT: B 258 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 354 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7476 (mp) REVERT: B 538 GLU cc_start: 0.7884 (mp0) cc_final: 0.7598 (mp0) REVERT: B 561 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8152 (mm-30) outliers start: 24 outliers final: 16 residues processed: 154 average time/residue: 1.6817 time to fit residues: 279.1267 Evaluate side-chains 155 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 413 ASN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102590 restraints weight = 13409.016| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.20 r_work: 0.3176 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13462 Z= 0.160 Angle : 0.569 7.035 18206 Z= 0.319 Chirality : 0.047 0.150 1858 Planarity : 0.004 0.040 2372 Dihedral : 5.324 46.464 1795 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.88 % Allowed : 14.60 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.56 (0.21), residues: 1618 helix: 1.10 (0.24), residues: 484 sheet: 1.03 (0.29), residues: 296 loop : -0.25 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE A 370 TYR 0.018 0.002 TYR B 14 ARG 0.009 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 572) hydrogen bonds : angle 5.61888 ( 1605) covalent geometry : bond 0.00356 (13462) covalent geometry : angle 0.56893 (18206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: A 354 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 538 GLU cc_start: 0.7957 (mp0) cc_final: 0.7699 (mp0) REVERT: B 91 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8218 (mtt180) REVERT: B 144 LYS cc_start: 0.8645 (tptp) cc_final: 0.8402 (tmtt) REVERT: B 258 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 354 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7507 (mp) REVERT: B 538 GLU cc_start: 0.7886 (mp0) cc_final: 0.7595 (mp0) REVERT: B 561 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8114 (mm-30) outliers start: 26 outliers final: 16 residues processed: 154 average time/residue: 1.6069 time to fit residues: 267.1318 Evaluate side-chains 158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102196 restraints weight = 13480.423| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.21 r_work: 0.3170 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13462 Z= 0.169 Angle : 0.580 7.107 18206 Z= 0.325 Chirality : 0.047 0.150 1858 Planarity : 0.004 0.039 2372 Dihedral : 5.361 45.359 1795 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.66 % Allowed : 14.81 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.54 (0.21), residues: 1618 helix: 1.07 (0.23), residues: 484 sheet: 1.05 (0.29), residues: 296 loop : -0.26 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE B 370 TYR 0.019 0.002 TYR A 14 ARG 0.008 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 572) hydrogen bonds : angle 5.64830 ( 1605) covalent geometry : bond 0.00379 (13462) covalent geometry : angle 0.58033 (18206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: A 290 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: A 354 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 538 GLU cc_start: 0.7945 (mp0) cc_final: 0.7683 (mp0) REVERT: B 91 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8213 (mtt180) REVERT: B 144 LYS cc_start: 0.8644 (tptp) cc_final: 0.8405 (tmtt) REVERT: B 258 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 354 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 538 GLU cc_start: 0.7887 (mp0) cc_final: 0.7585 (mp0) REVERT: B 561 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8113 (mm-30) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 1.5847 time to fit residues: 263.2045 Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 737 LYS Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 785 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 118 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 413 ASN B 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.083213 restraints weight = 13509.405| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.43 r_work: 0.2768 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13462 Z= 0.130 Angle : 0.535 6.694 18206 Z= 0.300 Chirality : 0.046 0.147 1858 Planarity : 0.004 0.040 2372 Dihedral : 5.191 45.983 1795 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.66 % Allowed : 14.96 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.61 (0.21), residues: 1618 helix: 1.19 (0.24), residues: 482 sheet: 1.07 (0.29), residues: 294 loop : -0.25 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 PHE 0.018 0.002 PHE B 370 TYR 0.015 0.001 TYR B 14 ARG 0.008 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 572) hydrogen bonds : angle 5.53080 ( 1605) covalent geometry : bond 0.00283 (13462) covalent geometry : angle 0.53538 (18206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11513.68 seconds wall clock time: 205 minutes 22.76 seconds (12322.76 seconds total)