Starting phenix.real_space_refine on Sun Aug 24 00:09:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bf8_7092/08_2025/6bf8_7092.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 43 5.16 5 C 9937 2.51 5 N 2589 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 15412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7748 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 897} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 7664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 939, 7664 Classifications: {'peptide': 939} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 49, 'TRANS': 889} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 3.11, per 1000 atoms: 0.20 Number of scatterers: 15412 At special positions: 0 Unit cell: (119.103, 119.103, 167.388, 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 43 16.00 O 2843 8.00 N 2589 7.00 C 9937 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: 0.95 Conformation dependent library (CDL) restraints added in 860.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 10 sheets defined 46.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.671A pdb=" N GLU A 59 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 60 " --> pdb=" O SER A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.679A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 157 through 167 removed outlier: 4.185A pdb=" N GLN A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.594A pdb=" N LYS A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.686A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.937A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.779A pdb=" N TYR A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 386 through 405 Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.688A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.699A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 5.243A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.704A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 677 through 690 Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.534A pdb=" N ALA A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 708 through 721 Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 801 through 815 removed outlier: 4.009A pdb=" N MET A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.676A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.557A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.588A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 removed outlier: 3.706A pdb=" N THR A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 929 " --> pdb=" O VAL A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 removed outlier: 3.826A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.527A pdb=" N SER B 98 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 99' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.860A pdb=" N PHE B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.850A pdb=" N PHE B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 removed outlier: 4.520A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.909A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 233' Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.693A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 4.440A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.590A pdb=" N GLY B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.787A pdb=" N GLU B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.688A pdb=" N HIS B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.779A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.950A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 516 removed outlier: 3.500A pdb=" N LYS B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.817A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.535A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.632A pdb=" N LYS B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 3.973A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 690 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 704 through 707 removed outlier: 3.809A pdb=" N VAL B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 708 through 721 Proline residue: B 717 - end of helix Processing helix chain 'B' and resid 735 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 3.926A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 855 through 876 Processing helix chain 'B' and resid 878 through 892 removed outlier: 3.663A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.558A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 930 removed outlier: 4.108A pdb=" N VAL B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 943 removed outlier: 3.855A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 999 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 69 removed outlier: 4.037A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 86 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 549 through 553 removed outlier: 6.380A pdb=" N LEU A 550 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE A 561 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 552 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP A 560 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N GLY A 731 " --> pdb=" O TRP A 560 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 777 removed outlier: 5.994A pdb=" N PHE A 777 " --> pdb=" O SER A 955 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS A 957 " --> pdb=" O PHE A 777 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 793 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 848 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.747A pdb=" N ARG B 65 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 258 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 151 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 365 Processing sheet with id=AA8, first strand: chain 'B' and resid 549 through 553 removed outlier: 5.216A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.626A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.626A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 954 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 794 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2049 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: 2.60 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4556 1.33 - 1.46: 3479 1.46 - 1.58: 7676 1.58 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 15797 Sorted by residual: bond pdb=" CB TRP A 513 " pdb=" CG TRP A 513 " ideal model delta sigma weight residual 1.498 1.427 0.071 3.10e-02 1.04e+03 5.30e+00 bond pdb=" C GLN A 638 " pdb=" N PRO A 639 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.38e-02 5.25e+03 5.14e+00 bond pdb=" C GLN B 638 " pdb=" N PRO B 639 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.08e+00 bond pdb=" CB TRP B 908 " pdb=" CG TRP B 908 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.71e+00 bond pdb=" CA ILE A 716 " pdb=" CB ILE A 716 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.95e+00 ... (remaining 15792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19682 2.13 - 4.26: 1430 4.26 - 6.39: 201 6.39 - 8.52: 40 8.52 - 10.65: 12 Bond angle restraints: 21365 Sorted by residual: angle pdb=" N HIS A 952 " pdb=" CA HIS A 952 " pdb=" C HIS A 952 " ideal model delta sigma weight residual 107.41 97.82 9.59 2.02e+00 2.45e-01 2.25e+01 angle pdb=" CA TRP A 776 " pdb=" CB TRP A 776 " pdb=" CG TRP A 776 " ideal model delta sigma weight residual 113.60 104.76 8.84 1.90e+00 2.77e-01 2.17e+01 angle pdb=" CA TYR A 685 " pdb=" CB TYR A 685 " pdb=" CG TYR A 685 " ideal model delta sigma weight residual 113.90 106.00 7.90 1.80e+00 3.09e-01 1.93e+01 angle pdb=" CA VAL B 272 " pdb=" CB VAL B 272 " pdb=" CG1 VAL B 272 " ideal model delta sigma weight residual 110.40 117.66 -7.26 1.70e+00 3.46e-01 1.83e+01 angle pdb=" N GLU A 453 " pdb=" CA GLU A 453 " pdb=" C GLU A 453 " ideal model delta sigma weight residual 113.02 106.73 6.29 1.49e+00 4.50e-01 1.78e+01 ... (remaining 21360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 8957 16.62 - 33.24: 483 33.24 - 49.86: 102 49.86 - 66.48: 9 66.48 - 83.10: 6 Dihedral angle restraints: 9557 sinusoidal: 3988 harmonic: 5569 Sorted by residual: dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LYS B 521 " pdb=" C LYS B 521 " pdb=" N PHE B 522 " pdb=" CA PHE B 522 " ideal model delta harmonic sigma weight residual -180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA LYS B 854 " pdb=" C LYS B 854 " pdb=" N PRO B 855 " pdb=" CA PRO B 855 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 9554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1715 0.069 - 0.137: 501 0.137 - 0.206: 68 0.206 - 0.275: 12 0.275 - 0.343: 4 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CB THR A 651 " pdb=" CA THR A 651 " pdb=" OG1 THR A 651 " pdb=" CG2 THR A 651 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA TYR A 685 " pdb=" N TYR A 685 " pdb=" C TYR A 685 " pdb=" CB TYR A 685 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CG LEU A 116 " pdb=" CB LEU A 116 " pdb=" CD1 LEU A 116 " pdb=" CD2 LEU A 116 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 2297 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 162 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C LEU B 162 " 0.066 2.00e-02 2.50e+03 pdb=" O LEU B 162 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 163 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 503 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLU B 503 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU B 503 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 504 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 503 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU A 503 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU A 503 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA A 504 " 0.019 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3329 2.78 - 3.31: 14600 3.31 - 3.84: 26498 3.84 - 4.37: 30775 4.37 - 4.90: 50774 Nonbonded interactions: 125976 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.252 3.040 nonbonded pdb=" OE1 GLN B 323 " pdb=" OH TYR B 444 " model vdw 2.282 3.040 nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 268 " model vdw 2.286 3.040 nonbonded pdb=" OE1 GLU A 145 " pdb=" OH TYR A 443 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP B 80 " pdb=" OG1 THR B 82 " model vdw 2.316 3.040 ... (remaining 125971 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 56 or resid 58 through 656 or (resid 657 and (n \ ame N or name CA or name C or name O or name CB )) or resid 658 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 719 or (resid 720 and (name N or name CA or name C or name O or name CB \ )) or resid 721 through 763 or (resid 764 through 765 and (name N or name CA or \ name C or name O or name CB )) or resid 766 through 888 or (resid 889 and (name \ N or name CA or name C or name CB )) or resid 890 through 962 or resid 989 throu \ gh 1011)) selection = (chain 'B' and (resid 46 through 541 or (resid 542 through 544 and (name N or na \ me CA or name C or name O or name CB )) or resid 545 through 1011)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.007 0.071 15797 Z= 0.335 Angle : 1.214 10.652 21365 Z= 0.678 Chirality : 0.064 0.343 2300 Planarity : 0.009 0.066 2761 Dihedral : 11.020 83.104 5957 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.13 (0.16), residues: 1878 helix: -3.03 (0.13), residues: 763 sheet: -1.53 (0.27), residues: 359 loop : -2.85 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 862 TYR 0.048 0.004 TYR A 858 PHE 0.033 0.004 PHE A 411 TRP 0.035 0.005 TRP B 199 HIS 0.012 0.003 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00699 (15797) covalent geometry : angle 1.21447 (21365) hydrogen bonds : bond 0.20018 ( 712) hydrogen bonds : angle 9.00659 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.9142 (tp30) cc_final: 0.8832 (pm20) REVERT: A 282 ASN cc_start: 0.9255 (t0) cc_final: 0.8951 (m110) REVERT: A 594 TYR cc_start: 0.7962 (t80) cc_final: 0.7658 (t80) REVERT: A 649 MET cc_start: 0.8451 (pp-130) cc_final: 0.8228 (ppp) REVERT: A 690 MET cc_start: 0.8385 (mmm) cc_final: 0.8163 (mmt) REVERT: A 704 LEU cc_start: 0.8161 (mt) cc_final: 0.7905 (tp) REVERT: A 858 TYR cc_start: 0.8764 (t80) cc_final: 0.8513 (t80) REVERT: B 309 ASP cc_start: 0.7768 (t0) cc_final: 0.7560 (m-30) REVERT: B 418 ASN cc_start: 0.8739 (m-40) cc_final: 0.8511 (p0) REVERT: B 422 PHE cc_start: 0.8206 (t80) cc_final: 0.7974 (t80) REVERT: B 466 MET cc_start: 0.8135 (tmm) cc_final: 0.7905 (tmm) REVERT: B 646 ILE cc_start: 0.8950 (mm) cc_final: 0.8496 (pt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1385 time to fit residues: 32.5362 Evaluate side-chains 82 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 245 HIS A 312 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS A 762 GLN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 297 HIS B 399 GLN B 519 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 821 ASN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.041816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.035749 restraints weight = 274693.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.036148 restraints weight = 223665.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.036373 restraints weight = 186472.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.036657 restraints weight = 160321.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.036843 restraints weight = 145928.794| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15797 Z= 0.189 Angle : 0.710 8.295 21365 Z= 0.378 Chirality : 0.044 0.174 2300 Planarity : 0.005 0.050 2761 Dihedral : 6.004 29.817 2050 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.18), residues: 1878 helix: -1.18 (0.16), residues: 811 sheet: -1.48 (0.27), residues: 360 loop : -2.38 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 200 TYR 0.030 0.002 TYR B 858 PHE 0.016 0.002 PHE B 777 TRP 0.027 0.002 TRP A 776 HIS 0.007 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00378 (15797) covalent geometry : angle 0.70991 (21365) hydrogen bonds : bond 0.04784 ( 712) hydrogen bonds : angle 6.46855 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 MET cc_start: 0.7764 (mtt) cc_final: 0.7495 (mtt) REVERT: A 704 LEU cc_start: 0.8094 (mt) cc_final: 0.7850 (mp) REVERT: A 744 MET cc_start: 0.7252 (tmm) cc_final: 0.6729 (tmm) REVERT: B 418 ASN cc_start: 0.8546 (m-40) cc_final: 0.8338 (p0) REVERT: B 422 PHE cc_start: 0.8365 (t80) cc_final: 0.8066 (t80) REVERT: B 466 MET cc_start: 0.8064 (tmm) cc_final: 0.7858 (tmm) REVERT: B 646 ILE cc_start: 0.8836 (mm) cc_final: 0.8605 (pt) REVERT: B 799 MET cc_start: 0.6729 (mtm) cc_final: 0.6528 (mtt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1233 time to fit residues: 18.2712 Evaluate side-chains 60 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 179 optimal weight: 0.0020 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.042082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.035896 restraints weight = 272989.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.036306 restraints weight = 221763.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.036589 restraints weight = 184860.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.036837 restraints weight = 162513.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.036935 restraints weight = 145237.556| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15797 Z= 0.129 Angle : 0.617 7.477 21365 Z= 0.324 Chirality : 0.042 0.156 2300 Planarity : 0.004 0.053 2761 Dihedral : 5.538 28.058 2050 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.18), residues: 1878 helix: -0.44 (0.17), residues: 816 sheet: -1.24 (0.27), residues: 355 loop : -2.18 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 368 TYR 0.025 0.001 TYR B 858 PHE 0.022 0.001 PHE A 659 TRP 0.017 0.001 TRP A 776 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00268 (15797) covalent geometry : angle 0.61729 (21365) hydrogen bonds : bond 0.04067 ( 712) hydrogen bonds : angle 5.86729 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 MET cc_start: 0.7518 (mtt) cc_final: 0.7134 (mtm) REVERT: A 704 LEU cc_start: 0.8152 (mt) cc_final: 0.7610 (tp) REVERT: A 744 MET cc_start: 0.7443 (tmm) cc_final: 0.7215 (tmm) REVERT: B 115 PHE cc_start: 0.6747 (t80) cc_final: 0.6132 (m-10) REVERT: B 490 ASP cc_start: 0.9320 (m-30) cc_final: 0.8962 (p0) REVERT: B 683 MET cc_start: 0.7051 (tmm) cc_final: 0.6695 (ttp) REVERT: B 943 MET cc_start: 0.6054 (tmm) cc_final: 0.5691 (tpt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1023 time to fit residues: 12.4723 Evaluate side-chains 60 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 166 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 HIS A 681 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 857 HIS ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 393 HIS B 589 HIS ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.041316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.035196 restraints weight = 275404.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.035597 restraints weight = 223251.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.035870 restraints weight = 186911.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.036104 restraints weight = 164483.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.036184 restraints weight = 148030.980| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15797 Z= 0.158 Angle : 0.640 8.840 21365 Z= 0.333 Chirality : 0.042 0.155 2300 Planarity : 0.004 0.049 2761 Dihedral : 5.459 28.790 2050 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1878 helix: -0.11 (0.18), residues: 819 sheet: -1.24 (0.27), residues: 343 loop : -1.99 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.024 0.002 TYR B 685 PHE 0.016 0.002 PHE A 659 TRP 0.021 0.002 TRP A 776 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00331 (15797) covalent geometry : angle 0.63960 (21365) hydrogen bonds : bond 0.03883 ( 712) hydrogen bonds : angle 5.59749 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 MET cc_start: 0.7687 (mtt) cc_final: 0.7332 (mtt) REVERT: A 704 LEU cc_start: 0.8249 (mt) cc_final: 0.7994 (mp) REVERT: A 744 MET cc_start: 0.7387 (tmm) cc_final: 0.7007 (tmm) REVERT: B 422 PHE cc_start: 0.8380 (t80) cc_final: 0.7981 (t80) REVERT: B 466 MET cc_start: 0.8307 (tmm) cc_final: 0.7989 (ptt) REVERT: B 592 MET cc_start: 0.6730 (mtp) cc_final: 0.6489 (mtp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1157 time to fit residues: 13.7639 Evaluate side-chains 55 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 79 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS A 336 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.041316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.035341 restraints weight = 276941.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.035735 restraints weight = 220717.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.035957 restraints weight = 184539.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.035957 restraints weight = 157225.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.035957 restraints weight = 157212.741| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15797 Z= 0.158 Angle : 0.631 10.624 21365 Z= 0.328 Chirality : 0.042 0.149 2300 Planarity : 0.004 0.048 2761 Dihedral : 5.431 27.140 2050 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.19), residues: 1878 helix: 0.01 (0.18), residues: 819 sheet: -1.19 (0.27), residues: 352 loop : -1.83 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 368 TYR 0.022 0.002 TYR B 685 PHE 0.015 0.002 PHE A 659 TRP 0.020 0.002 TRP A 776 HIS 0.005 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00335 (15797) covalent geometry : angle 0.63056 (21365) hydrogen bonds : bond 0.03801 ( 712) hydrogen bonds : angle 5.51756 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 704 LEU cc_start: 0.8293 (mt) cc_final: 0.8056 (mp) REVERT: A 744 MET cc_start: 0.7436 (tmm) cc_final: 0.6891 (tmm) REVERT: B 592 MET cc_start: 0.6934 (mtp) cc_final: 0.6702 (mtp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0960 time to fit residues: 11.2224 Evaluate side-chains 53 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 121 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 252 ASN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.040576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.034612 restraints weight = 275781.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.034993 restraints weight = 224945.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.035285 restraints weight = 187061.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.035453 restraints weight = 161994.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.035676 restraints weight = 145932.512| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15797 Z= 0.204 Angle : 0.717 10.789 21365 Z= 0.374 Chirality : 0.044 0.192 2300 Planarity : 0.005 0.045 2761 Dihedral : 5.773 27.272 2050 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.19), residues: 1878 helix: -0.19 (0.17), residues: 818 sheet: -1.26 (0.28), residues: 333 loop : -1.85 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 423 TYR 0.029 0.002 TYR B 685 PHE 0.021 0.002 PHE B 522 TRP 0.024 0.002 TRP A 776 HIS 0.009 0.002 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00427 (15797) covalent geometry : angle 0.71722 (21365) hydrogen bonds : bond 0.04071 ( 712) hydrogen bonds : angle 5.72059 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 MET cc_start: 0.7821 (mtt) cc_final: 0.7306 (mtm) REVERT: A 627 MET cc_start: 0.8277 (tpp) cc_final: 0.7951 (tpp) REVERT: A 690 MET cc_start: 0.8870 (tpp) cc_final: 0.8579 (tpp) REVERT: A 704 LEU cc_start: 0.8439 (mt) cc_final: 0.8190 (mp) REVERT: B 466 MET cc_start: 0.8436 (tmm) cc_final: 0.8121 (ptt) REVERT: B 592 MET cc_start: 0.7261 (mtp) cc_final: 0.7020 (mtp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0974 time to fit residues: 10.5406 Evaluate side-chains 53 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 109 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 190 HIS ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 HIS A 363 GLN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS B 762 GLN ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.039172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.032051 restraints weight = 312705.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.032364 restraints weight = 265489.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.032548 restraints weight = 234006.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.032734 restraints weight = 212477.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.032941 restraints weight = 198444.948| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15797 Z= 0.315 Angle : 0.937 12.275 21365 Z= 0.493 Chirality : 0.050 0.184 2300 Planarity : 0.007 0.087 2761 Dihedral : 6.983 28.208 2050 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 34.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.18), residues: 1878 helix: -1.17 (0.16), residues: 817 sheet: -1.67 (0.27), residues: 327 loop : -2.27 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 200 TYR 0.044 0.003 TYR A 314 PHE 0.027 0.004 PHE A 673 TRP 0.030 0.003 TRP A 776 HIS 0.016 0.003 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00654 (15797) covalent geometry : angle 0.93734 (21365) hydrogen bonds : bond 0.05299 ( 712) hydrogen bonds : angle 6.53282 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.7625 (mpp) cc_final: 0.7289 (mpp) REVERT: A 592 MET cc_start: 0.7752 (mtt) cc_final: 0.7301 (mtm) REVERT: A 690 MET cc_start: 0.8769 (tpp) cc_final: 0.8141 (tpp) REVERT: A 704 LEU cc_start: 0.8738 (mt) cc_final: 0.8319 (pp) REVERT: A 870 MET cc_start: 0.9304 (tpt) cc_final: 0.8959 (tpp) REVERT: B 113 MET cc_start: 0.4031 (mmp) cc_final: 0.3639 (mmm) REVERT: B 592 MET cc_start: 0.7580 (mtp) cc_final: 0.7186 (mtp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0964 time to fit residues: 10.3156 Evaluate side-chains 51 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 167 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.040719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.034709 restraints weight = 276090.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.035064 restraints weight = 223793.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.035284 restraints weight = 187275.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.035528 restraints weight = 167273.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.035655 restraints weight = 150345.610| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15797 Z= 0.150 Angle : 0.687 10.263 21365 Z= 0.356 Chirality : 0.044 0.213 2300 Planarity : 0.005 0.047 2761 Dihedral : 6.159 28.628 2050 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.18), residues: 1878 helix: -0.51 (0.17), residues: 826 sheet: -1.31 (0.28), residues: 331 loop : -2.04 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.020 0.002 TYR B 609 PHE 0.017 0.002 PHE A 293 TRP 0.019 0.002 TRP B 776 HIS 0.007 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00321 (15797) covalent geometry : angle 0.68723 (21365) hydrogen bonds : bond 0.04004 ( 712) hydrogen bonds : angle 5.94117 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.7524 (mpp) cc_final: 0.7120 (mpp) REVERT: A 592 MET cc_start: 0.7650 (mtt) cc_final: 0.7088 (mtm) REVERT: A 690 MET cc_start: 0.8912 (tpp) cc_final: 0.8330 (tpp) REVERT: A 704 LEU cc_start: 0.8292 (mt) cc_final: 0.7792 (pp) REVERT: A 744 MET cc_start: 0.8011 (tmm) cc_final: 0.7706 (tmm) REVERT: A 870 MET cc_start: 0.8787 (tpt) cc_final: 0.8510 (tpp) REVERT: B 466 MET cc_start: 0.8434 (tmm) cc_final: 0.8029 (ptt) REVERT: B 592 MET cc_start: 0.7323 (mtp) cc_final: 0.6919 (mtp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0951 time to fit residues: 10.5857 Evaluate side-chains 52 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 99 optimal weight: 0.2980 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 575 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 245 HIS ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN B 718 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.041145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.035078 restraints weight = 273354.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.035521 restraints weight = 217450.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.035751 restraints weight = 178608.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.036043 restraints weight = 151040.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.036120 restraints weight = 137597.339| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15797 Z= 0.122 Angle : 0.632 8.438 21365 Z= 0.325 Chirality : 0.044 0.209 2300 Planarity : 0.004 0.048 2761 Dihedral : 5.589 25.790 2050 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.19), residues: 1878 helix: -0.04 (0.17), residues: 818 sheet: -1.12 (0.28), residues: 333 loop : -1.81 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 368 TYR 0.015 0.001 TYR A 685 PHE 0.017 0.002 PHE A 293 TRP 0.011 0.001 TRP B 776 HIS 0.006 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00259 (15797) covalent geometry : angle 0.63207 (21365) hydrogen bonds : bond 0.03528 ( 712) hydrogen bonds : angle 5.56754 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.6758 (pmm) cc_final: 0.6547 (pmm) REVERT: A 254 MET cc_start: 0.7426 (mpp) cc_final: 0.7082 (mpp) REVERT: A 690 MET cc_start: 0.8913 (tpp) cc_final: 0.8461 (tpp) REVERT: A 704 LEU cc_start: 0.8203 (mt) cc_final: 0.7726 (pp) REVERT: A 744 MET cc_start: 0.7744 (tmm) cc_final: 0.7447 (tmm) REVERT: A 870 MET cc_start: 0.8630 (tpt) cc_final: 0.8397 (tpp) REVERT: B 592 MET cc_start: 0.7239 (mtp) cc_final: 0.6844 (mtp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1184 time to fit residues: 12.9096 Evaluate side-chains 52 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 168 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN A 788 ASN ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.039821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.032615 restraints weight = 307174.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.032964 restraints weight = 259832.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.033266 restraints weight = 222182.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.033447 restraints weight = 194597.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.033505 restraints weight = 182602.215| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15797 Z= 0.211 Angle : 0.742 11.107 21365 Z= 0.385 Chirality : 0.046 0.256 2300 Planarity : 0.005 0.051 2761 Dihedral : 6.052 28.654 2050 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.18), residues: 1878 helix: -0.39 (0.17), residues: 820 sheet: -1.34 (0.28), residues: 335 loop : -1.92 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 687 TYR 0.026 0.002 TYR A 314 PHE 0.022 0.002 PHE A 673 TRP 0.024 0.002 TRP A 776 HIS 0.008 0.002 HIS B 885 Details of bonding type rmsd covalent geometry : bond 0.00441 (15797) covalent geometry : angle 0.74168 (21365) hydrogen bonds : bond 0.04105 ( 712) hydrogen bonds : angle 5.82187 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3756 Ramachandran restraints generated. 1878 Oldfield, 0 Emsley, 1878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 690 MET cc_start: 0.8684 (tpp) cc_final: 0.8237 (tpp) REVERT: A 704 LEU cc_start: 0.8316 (mt) cc_final: 0.7918 (pp) REVERT: A 744 MET cc_start: 0.7498 (tmm) cc_final: 0.7108 (tmm) REVERT: A 963 MET cc_start: 0.7702 (tpt) cc_final: 0.7408 (tpt) REVERT: B 592 MET cc_start: 0.7314 (mtp) cc_final: 0.6814 (mtp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1109 time to fit residues: 11.2163 Evaluate side-chains 51 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 72 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.040472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.034559 restraints weight = 278814.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.034955 restraints weight = 225392.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.035141 restraints weight = 186890.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.035346 restraints weight = 164900.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.035346 restraints weight = 146827.388| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15797 Z= 0.178 Angle : 0.704 9.844 21365 Z= 0.363 Chirality : 0.044 0.195 2300 Planarity : 0.005 0.051 2761 Dihedral : 5.997 26.996 2050 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.19), residues: 1878 helix: -0.38 (0.17), residues: 825 sheet: -1.27 (0.28), residues: 330 loop : -1.92 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.019 0.002 TYR A 454 PHE 0.020 0.002 PHE A 673 TRP 0.021 0.002 TRP A 776 HIS 0.007 0.002 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00374 (15797) covalent geometry : angle 0.70382 (21365) hydrogen bonds : bond 0.03939 ( 712) hydrogen bonds : angle 5.83095 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.69 seconds wall clock time: 39 minutes 1.34 seconds (2341.34 seconds total)