Starting phenix.real_space_refine on Sat Aug 23 16:58:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho9_34923/08_2025/8ho9_34923_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho9_34923/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ho9_34923/08_2025/8ho9_34923_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho9_34923/08_2025/8ho9_34923_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ho9_34923/08_2025/8ho9_34923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho9_34923/08_2025/8ho9_34923.map" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.00, per 1000 atoms: 0.22 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: 0.94 Conformation dependent library (CDL) restraints added in 421.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.43 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: 2.21 Time building geometry restraints manager: 1.27 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: 0.02 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: 4.990 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- 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 : 2.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 377 TYR 0.016 0.002 TYR A 14 PHE 0.014 0.002 PHE B 360 TRP 0.016 0.002 TRP B 332 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00859 (13462) covalent geometry : angle 0.69217 (18206) hydrogen bonds : bond 0.12048 ( 572) hydrogen bonds : angle 6.42635 ( 1605) *********************** 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 : 0.485 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: 0.7035 time to fit residues: 110.7847 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 : 0.337 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.119212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103636 restraints weight = 13471.326| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.21 r_work: 0.3190 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13462 Z= 0.132 Angle : 0.547 6.453 18206 Z= 0.307 Chirality : 0.046 0.147 1858 Planarity : 0.004 0.041 2372 Dihedral : 6.488 56.973 1819 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.17 % Allowed : 13.22 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1618 helix: 0.94 (0.24), residues: 490 sheet: 0.88 (0.29), residues: 304 loop : -0.24 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 540 TYR 0.016 0.001 TYR B 14 PHE 0.019 0.002 PHE A 370 TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00282 (13462) covalent geometry : angle 0.54717 (18206) hydrogen bonds : bond 0.04713 ( 572) hydrogen bonds : angle 5.70131 ( 1605) *********************** 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 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.438 Fit side-chains REVERT: A 142 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7993 (tttm) REVERT: A 536 GLU cc_start: 0.7296 (mp0) cc_final: 0.7091 (mm-30) REVERT: B 142 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8188 (tttp) REVERT: B 544 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8119 (mt0) outliers start: 30 outliers final: 16 residues processed: 153 average time/residue: 0.6842 time to fit residues: 112.9148 Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 402 LEU 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 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 544 GLN 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 86 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101160 restraints weight = 13617.682| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.22 r_work: 0.3153 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13462 Z= 0.198 Angle : 0.612 7.345 18206 Z= 0.343 Chirality : 0.049 0.151 1858 Planarity : 0.005 0.045 2372 Dihedral : 6.212 55.282 1802 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.82 % Allowed : 13.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.21), residues: 1618 helix: 0.87 (0.24), residues: 486 sheet: 0.98 (0.29), residues: 296 loop : -0.32 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 377 TYR 0.020 0.002 TYR B 14 PHE 0.018 0.002 PHE A 370 TRP 0.023 0.003 TRP B 332 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00447 (13462) covalent geometry : angle 0.61240 (18206) hydrogen bonds : bond 0.05572 ( 572) hydrogen bonds : angle 5.80573 ( 1605) *********************** 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 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.396 Fit side-chains REVERT: A 258 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: A 315 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.7781 (mmtp) REVERT: A 536 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: B 258 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 290 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: B 544 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 561 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8120 (mm-30) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 0.6472 time to fit residues: 111.0793 Evaluate side-chains 159 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 315 LYS Chi-restraints excluded: chain A residue 374 ILE 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 87 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 374 ILE 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 544 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.116137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100490 restraints weight = 13467.652| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.21 r_work: 0.3144 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13462 Z= 0.228 Angle : 0.646 7.687 18206 Z= 0.362 Chirality : 0.050 0.151 1858 Planarity : 0.005 0.050 2372 Dihedral : 6.324 53.623 1802 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 12.57 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.21), residues: 1618 helix: 0.76 (0.23), residues: 486 sheet: 1.01 (0.29), residues: 296 loop : -0.34 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 377 TYR 0.021 0.002 TYR B 14 PHE 0.018 0.003 PHE A 370 TRP 0.025 0.003 TRP A 332 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00522 (13462) covalent geometry : angle 0.64586 (18206) hydrogen bonds : bond 0.05919 ( 572) hydrogen bonds : angle 5.86345 ( 1605) *********************** 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 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.379 Fit side-chains REVERT: A 142 LYS cc_start: 0.8313 (mtpp) cc_final: 0.8077 (tttm) REVERT: A 258 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: A 315 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.7822 (mmtp) REVERT: A 536 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: B 32 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: B 91 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8215 (mtt180) REVERT: B 258 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 290 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: B 561 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8115 (mm-30) outliers start: 43 outliers final: 24 residues processed: 165 average time/residue: 0.6486 time to fit residues: 115.4483 Evaluate side-chains 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 315 LYS Chi-restraints excluded: chain A residue 374 ILE 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 32 GLU 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 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 374 ILE 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 32 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.116228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100584 restraints weight = 13558.010| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.21 r_work: 0.3145 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13462 Z= 0.218 Angle : 0.633 7.449 18206 Z= 0.356 Chirality : 0.050 0.151 1858 Planarity : 0.005 0.046 2372 Dihedral : 6.258 53.652 1802 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.11 % Allowed : 12.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.21), residues: 1618 helix: 0.75 (0.23), residues: 486 sheet: 1.02 (0.29), residues: 296 loop : -0.34 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 377 TYR 0.020 0.002 TYR A 14 PHE 0.018 0.002 PHE A 370 TRP 0.025 0.003 TRP A 332 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00496 (13462) covalent geometry : angle 0.63346 (18206) hydrogen bonds : bond 0.05757 ( 572) hydrogen bonds : angle 5.82460 ( 1605) *********************** 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 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.333 Fit side-chains REVERT: A 142 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8078 (tttm) REVERT: A 258 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: A 290 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: A 315 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.7807 (mmtp) REVERT: A 536 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7361 (mm-30) REVERT: B 91 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8227 (mtt180) REVERT: B 258 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: B 290 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: B 561 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8113 (mm-30) outliers start: 43 outliers final: 25 residues processed: 165 average time/residue: 0.6463 time to fit residues: 115.2727 Evaluate side-chains 164 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 374 ILE 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 87 SER 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 290 GLU Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 374 ILE 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 766 THR 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 2 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102272 restraints weight = 13548.845| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.21 r_work: 0.3170 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0770 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= 0.155 Angle : 0.568 6.896 18206 Z= 0.320 Chirality : 0.047 0.149 1858 Planarity : 0.004 0.042 2372 Dihedral : 5.943 50.867 1802 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.38 % Allowed : 13.95 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1618 helix: 0.94 (0.24), residues: 484 sheet: 1.01 (0.29), residues: 296 loop : -0.33 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 377 TYR 0.017 0.002 TYR B 14 PHE 0.018 0.002 PHE A 370 TRP 0.023 0.002 TRP B 332 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00343 (13462) covalent geometry : angle 0.56800 (18206) hydrogen bonds : bond 0.04970 ( 572) hydrogen bonds : angle 5.67348 ( 1605) *********************** 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 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.475 Fit side-chains REVERT: A 142 LYS cc_start: 0.8254 (mtpp) cc_final: 0.8045 (tttp) REVERT: A 258 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: A 538 GLU cc_start: 0.7884 (mp0) cc_final: 0.7592 (mp0) REVERT: B 91 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8201 (mtt180) REVERT: B 258 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: B 561 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8109 (mm-30) outliers start: 33 outliers final: 21 residues processed: 161 average time/residue: 0.6727 time to fit residues: 116.7634 Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 374 ILE 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 524 LYS Chi-restraints excluded: chain A residue 721 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 66 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.117297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101649 restraints weight = 13481.182| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.21 r_work: 0.3161 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.0771 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= 0.175 Angle : 0.591 7.221 18206 Z= 0.332 Chirality : 0.048 0.150 1858 Planarity : 0.005 0.042 2372 Dihedral : 5.897 50.435 1801 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.67 % Allowed : 13.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.21), residues: 1618 helix: 0.88 (0.24), residues: 486 sheet: 1.02 (0.29), residues: 296 loop : -0.33 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 377 TYR 0.019 0.002 TYR A 14 PHE 0.017 0.002 PHE A 370 TRP 0.023 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00393 (13462) covalent geometry : angle 0.59067 (18206) hydrogen bonds : bond 0.05232 ( 572) hydrogen bonds : angle 5.71560 ( 1605) *********************** 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 172 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.549 Fit side-chains REVERT: A 142 LYS cc_start: 0.8255 (mtpp) cc_final: 0.8048 (tttp) REVERT: A 258 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: A 290 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: A 315 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.7783 (mmtp) REVERT: A 538 GLU cc_start: 0.7904 (mp0) cc_final: 0.7644 (mp0) REVERT: B 91 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8210 (mtt180) REVERT: B 258 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: B 290 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: B 561 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8124 (mm-30) outliers start: 37 outliers final: 24 residues processed: 166 average time/residue: 0.6385 time to fit residues: 115.0832 Evaluate side-chains 163 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 290 GLU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 374 ILE 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 524 LYS Chi-restraints excluded: chain A residue 721 THR 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 154 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 310 ASN 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 528 LYS Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 721 THR 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 98 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.120280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104718 restraints weight = 13460.891| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.21 r_work: 0.3205 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0881 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= 0.113 Angle : 0.515 6.444 18206 Z= 0.289 Chirality : 0.045 0.144 1858 Planarity : 0.004 0.042 2372 Dihedral : 5.418 45.926 1801 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.88 % Allowed : 14.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1618 helix: 1.13 (0.24), residues: 488 sheet: 1.05 (0.29), residues: 294 loop : -0.22 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 377 TYR 0.014 0.001 TYR B 14 PHE 0.018 0.001 PHE A 370 TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00240 (13462) covalent geometry : angle 0.51473 (18206) hydrogen bonds : bond 0.04157 ( 572) hydrogen bonds : angle 5.48310 ( 1605) *********************** 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 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 290 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 538 GLU cc_start: 0.7912 (mp0) cc_final: 0.7663 (mp0) REVERT: B 91 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8159 (mtt180) REVERT: B 258 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 538 GLU cc_start: 0.7834 (mp0) cc_final: 0.7567 (mp0) REVERT: B 561 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8106 (mm-30) outliers start: 26 outliers final: 15 residues processed: 160 average time/residue: 0.7070 time to fit residues: 121.7811 Evaluate side-chains 153 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 518 MET 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 87 SER 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 518 MET Chi-restraints excluded: chain B residue 528 LYS 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 18 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.117417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101713 restraints weight = 13591.893| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.22 r_work: 0.3164 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0807 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= 0.182 Angle : 0.593 7.314 18206 Z= 0.332 Chirality : 0.048 0.149 1858 Planarity : 0.005 0.042 2372 Dihedral : 5.526 45.369 1796 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.10 % Allowed : 14.96 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1618 helix: 1.02 (0.23), residues: 484 sheet: 1.03 (0.29), residues: 296 loop : -0.27 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 377 TYR 0.019 0.002 TYR A 14 PHE 0.017 0.002 PHE A 370 TRP 0.022 0.002 TRP A 332 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00410 (13462) covalent geometry : angle 0.59254 (18206) hydrogen bonds : bond 0.05242 ( 572) hydrogen bonds : angle 5.68800 ( 1605) *********************** 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 171 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.472 Fit side-chains REVERT: A 258 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: A 290 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: A 354 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7642 (mp) REVERT: A 538 GLU cc_start: 0.7989 (mp0) cc_final: 0.7609 (mp0) REVERT: B 91 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8202 (mtt180) REVERT: B 258 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: B 538 GLU cc_start: 0.7934 (mp0) cc_final: 0.7637 (mp0) REVERT: B 544 GLN cc_start: 0.8463 (mt0) cc_final: 0.8113 (mt0) REVERT: B 561 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8093 (mm-30) outliers start: 29 outliers final: 19 residues processed: 160 average time/residue: 0.7205 time to fit residues: 124.4578 Evaluate side-chains 157 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 LYS 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 87 SER 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 363 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 528 LYS 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 18 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.117901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102232 restraints weight = 13486.954| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.21 r_work: 0.3169 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13462 Z= 0.166 Angle : 0.581 7.095 18206 Z= 0.326 Chirality : 0.047 0.150 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.491 46.222 1796 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.38 % Allowed : 14.74 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1618 helix: 1.03 (0.23), residues: 484 sheet: 1.03 (0.29), residues: 296 loop : -0.26 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 377 TYR 0.018 0.002 TYR A 14 PHE 0.018 0.002 PHE A 370 TRP 0.022 0.002 TRP B 332 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00371 (13462) covalent geometry : angle 0.58051 (18206) hydrogen bonds : bond 0.05033 ( 572) hydrogen bonds : angle 5.66324 ( 1605) ********************** 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 169 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.414 Fit side-chains REVERT: A 258 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: A 290 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8456 (tm-30) REVERT: A 354 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7647 (mp) REVERT: A 356 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5570 (mtt180) REVERT: A 538 GLU cc_start: 0.7988 (mp0) cc_final: 0.7712 (mp0) REVERT: B 91 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8205 (mtt180) REVERT: B 258 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: B 354 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7550 (mp) REVERT: B 538 GLU cc_start: 0.7925 (mp0) cc_final: 0.7628 (mp0) REVERT: B 544 GLN cc_start: 0.8461 (mt0) cc_final: 0.8026 (mt0) REVERT: B 561 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8110 (mm-30) outliers start: 33 outliers final: 22 residues processed: 157 average time/residue: 0.6929 time to fit residues: 117.1704 Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 356 ARG Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 737 LYS 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 87 SER 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 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 528 LYS 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 75 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.118911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103228 restraints weight = 13602.260| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.22 r_work: 0.3185 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13462 Z= 0.138 Angle : 0.549 6.844 18206 Z= 0.308 Chirality : 0.046 0.148 1858 Planarity : 0.004 0.041 2372 Dihedral : 5.330 45.608 1796 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.88 % Allowed : 15.17 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.21), residues: 1618 helix: 1.10 (0.24), residues: 484 sheet: 1.07 (0.29), residues: 294 loop : -0.24 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 377 TYR 0.016 0.002 TYR A 14 PHE 0.018 0.002 PHE A 370 TRP 0.021 0.002 TRP B 332 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00302 (13462) covalent geometry : angle 0.54863 (18206) hydrogen bonds : bond 0.04604 ( 572) hydrogen bonds : angle 5.57228 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4172.10 seconds wall clock time: 71 minutes 53.83 seconds (4313.83 seconds total)