Starting phenix.real_space_refine on Sat Mar 16 18:52:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_7092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_7092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_7092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_7092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bf8_7092/03_2024/6bf8_7092.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 767": "NH1" <-> "NH2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B ARG 892": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 7.18, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 5.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.74 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: 5.36 Time building geometry restraints manager: 6.30 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: 97.04 - 104.44: 306 104.44 - 111.83: 6858 111.83 - 119.22: 5952 119.22 - 126.62: 8034 126.62 - 134.01: 215 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 2.440 nonbonded pdb=" OE1 GLN B 323 " pdb=" OH TYR B 444 " model vdw 2.282 2.440 nonbonded pdb=" O LEU A 264 " pdb=" OG1 THR A 268 " model vdw 2.286 2.440 nonbonded pdb=" OE1 GLU A 145 " pdb=" OH TYR A 443 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASP B 80 " pdb=" OG1 THR B 82 " model vdw 2.316 2.440 ... (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 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: 1.620 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: 7.340 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.230 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.460 ------------------------------------------------------------------------------- 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= 0.448 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.005 TRP B 199 HIS 0.012 0.003 HIS A 340 PHE 0.033 0.004 PHE A 411 TYR 0.048 0.004 TYR A 858 ARG 0.015 0.001 ARG A 862 *********************** 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 fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.943 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: A 176 GLU cc_start: 0.9142 (tp30) cc_final: 0.8856 (pm20) REVERT: A 282 ASN cc_start: 0.9255 (t0) cc_final: 0.9012 (m-40) 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: 0.8229 (ppp) REVERT: A 690 MET cc_start: 0.8385 (mmm) cc_final: 0.7985 (mmt) REVERT: A 704 LEU cc_start: 0.8161 (mt) cc_final: 0.7904 (tp) 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: 0.8505 (p0) REVERT: B 422 PHE cc_start: 0.8206 (t80) cc_final: 0.7942 (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: 0.8495 (pt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3533 time to fit residues: 82.5958 Evaluate side-chains 80 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 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 297 HIS B 399 GLN B 515 ASN 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 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2203 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= 0.191 Angle : 0.663 7.880 21365 Z= 0.352 Chirality : 0.043 0.175 2300 Planarity : 0.005 0.047 2761 Dihedral : 5.829 25.876 2050 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.18), residues: 1878 helix: -1.17 (0.16), residues: 807 sheet: -1.28 (0.27), residues: 357 loop : -2.39 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 776 HIS 0.006 0.001 HIS A 157 PHE 0.013 0.001 PHE A 939 TYR 0.031 0.002 TYR B 858 ARG 0.008 0.001 ARG A 711 *********************** 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 fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.872 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 254 MET cc_start: 0.8149 (mpp) cc_final: 0.7755 (mpp) REVERT: A 282 ASN cc_start: 0.9313 (t0) cc_final: 0.9024 (m110) REVERT: A 594 TYR cc_start: 0.8142 (t80) cc_final: 0.7830 (t80) REVERT: A 690 MET cc_start: 0.8216 (mmm) cc_final: 0.7913 (mmt) REVERT: A 704 LEU cc_start: 0.8373 (mt) cc_final: 0.7896 (tp) REVERT: A 744 MET cc_start: 0.8000 (tmm) cc_final: 0.7524 (tmm) REVERT: B 113 MET cc_start: 0.2295 (mmm) cc_final: 0.1933 (mmm) REVERT: B 115 PHE cc_start: 0.7457 (t80) cc_final: 0.6575 (m-10) REVERT: B 422 PHE cc_start: 0.8266 (t80) cc_final: 0.7952 (t80) REVERT: B 466 MET cc_start: 0.8099 (tmm) cc_final: 0.7870 (tmm) REVERT: B 646 ILE cc_start: 0.8879 (mm) cc_final: 0.8592 (pt) REVERT: B 943 MET cc_start: 0.6255 (tmm) cc_final: 0.5853 (tpt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2876 time to fit residues: 42.6236 Evaluate side-chains 67 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 730 HIS ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS ** A 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** B 157 HIS ** 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B 915 GLN ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15797 Z= 0.317 Angle : 0.756 8.247 21365 Z= 0.403 Chirality : 0.044 0.155 2300 Planarity : 0.005 0.047 2761 Dihedral : 6.050 26.465 2050 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.18), residues: 1878 helix: -0.63 (0.17), residues: 808 sheet: -1.40 (0.27), residues: 348 loop : -2.26 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 776 HIS 0.009 0.002 HIS A 291 PHE 0.031 0.003 PHE B 777 TYR 0.030 0.002 TYR B 685 ARG 0.004 0.001 ARG A 711 *********************** 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 76 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8105 (mpp) cc_final: 0.7710 (mpp) REVERT: A 282 ASN cc_start: 0.9448 (t0) cc_final: 0.9205 (m-40) REVERT: A 627 MET cc_start: 0.8041 (tpt) cc_final: 0.7794 (tpt) REVERT: A 690 MET cc_start: 0.8207 (mmm) cc_final: 0.7886 (mmt) REVERT: B 466 MET cc_start: 0.8140 (tmm) cc_final: 0.7926 (tmm) REVERT: B 592 MET cc_start: 0.7174 (mtp) cc_final: 0.6816 (mtp) REVERT: B 824 ARG cc_start: 0.7313 (ttt180) cc_final: 0.7105 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2793 time to fit residues: 33.3183 Evaluate side-chains 55 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 170 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 573 ASN 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 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** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15797 Z= 0.315 Angle : 0.779 11.035 21365 Z= 0.410 Chirality : 0.045 0.175 2300 Planarity : 0.005 0.047 2761 Dihedral : 6.287 27.696 2050 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.12 % Allowed : 3.18 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 1878 helix: -0.57 (0.17), residues: 811 sheet: -1.37 (0.28), residues: 334 loop : -2.26 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 776 HIS 0.009 0.002 HIS A 291 PHE 0.023 0.003 PHE A 777 TYR 0.035 0.003 TYR B 685 ARG 0.005 0.001 ARG B 181 *********************** 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 74 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8014 (mpp) cc_final: 0.7614 (mpp) REVERT: A 282 ASN cc_start: 0.9450 (t0) cc_final: 0.9213 (m-40) REVERT: A 690 MET cc_start: 0.8132 (mmm) cc_final: 0.7839 (mmt) REVERT: A 870 MET cc_start: 0.8425 (tpt) cc_final: 0.8219 (tpp) REVERT: B 466 MET cc_start: 0.8180 (tmm) cc_final: 0.7961 (tmm) REVERT: B 592 MET cc_start: 0.7593 (mtp) cc_final: 0.7192 (mtp) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.2724 time to fit residues: 32.1144 Evaluate side-chains 58 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 162 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 overall best weight: 2.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** 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 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15797 Z= 0.179 Angle : 0.624 9.817 21365 Z= 0.324 Chirality : 0.043 0.165 2300 Planarity : 0.004 0.043 2761 Dihedral : 5.732 23.871 2050 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.19), residues: 1878 helix: -0.06 (0.18), residues: 803 sheet: -1.14 (0.27), residues: 351 loop : -1.98 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 776 HIS 0.005 0.001 HIS B 885 PHE 0.032 0.002 PHE A 811 TYR 0.020 0.001 TYR B 858 ARG 0.004 0.000 ARG B 368 *********************** 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 73 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.748 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 254 MET cc_start: 0.8103 (mpp) cc_final: 0.7649 (mpp) REVERT: A 282 ASN cc_start: 0.9434 (t0) cc_final: 0.9180 (m-40) REVERT: A 690 MET cc_start: 0.8151 (mmm) cc_final: 0.7844 (mmp) REVERT: A 744 MET cc_start: 0.8019 (tmm) cc_final: 0.7598 (tmm) REVERT: A 870 MET cc_start: 0.8392 (tpt) cc_final: 0.8173 (tpp) REVERT: B 466 MET cc_start: 0.8159 (tmm) cc_final: 0.7954 (tmm) REVERT: B 592 MET cc_start: 0.7402 (mtp) cc_final: 0.7156 (mtp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2638 time to fit residues: 30.9806 Evaluate side-chains 55 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 HIS ** B 957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15797 Z= 0.203 Angle : 0.635 10.088 21365 Z= 0.329 Chirality : 0.043 0.167 2300 Planarity : 0.004 0.043 2761 Dihedral : 5.657 25.457 2050 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1878 helix: 0.06 (0.18), residues: 805 sheet: -1.11 (0.28), residues: 338 loop : -1.90 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 776 HIS 0.005 0.001 HIS B 885 PHE 0.019 0.002 PHE A 811 TYR 0.019 0.002 TYR B 685 ARG 0.004 0.000 ARG B 368 *********************** 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 67 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8034 (mpp) cc_final: 0.7526 (mpp) REVERT: A 282 ASN cc_start: 0.9411 (t0) cc_final: 0.9152 (m-40) REVERT: A 690 MET cc_start: 0.8073 (mmm) cc_final: 0.7798 (mmt) REVERT: A 744 MET cc_start: 0.8021 (tmm) cc_final: 0.7513 (tmm) REVERT: A 870 MET cc_start: 0.8438 (tpt) cc_final: 0.8178 (tpp) REVERT: B 466 MET cc_start: 0.8215 (tmm) cc_final: 0.7893 (tmm) REVERT: B 592 MET cc_start: 0.7574 (mtp) cc_final: 0.7304 (mtp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2632 time to fit residues: 29.1314 Evaluate side-chains 53 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 180 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 overall best weight: 6.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** 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 851 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15797 Z= 0.351 Angle : 0.820 9.409 21365 Z= 0.431 Chirality : 0.047 0.160 2300 Planarity : 0.006 0.067 2761 Dihedral : 6.470 25.246 2050 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.18), residues: 1878 helix: -0.56 (0.17), residues: 811 sheet: -1.41 (0.27), residues: 340 loop : -2.09 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 776 HIS 0.012 0.002 HIS A 291 PHE 0.023 0.003 PHE A 673 TYR 0.038 0.003 TYR A 314 ARG 0.009 0.001 ARG A 423 *********************** 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 63 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.768 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 254 MET cc_start: 0.7950 (mpp) cc_final: 0.7439 (mpp) REVERT: A 282 ASN cc_start: 0.9461 (t0) cc_final: 0.9203 (m-40) REVERT: A 690 MET cc_start: 0.7969 (mmm) cc_final: 0.7748 (mmt) REVERT: A 870 MET cc_start: 0.8457 (tpt) cc_final: 0.8218 (tpp) REVERT: B 466 MET cc_start: 0.8235 (tmm) cc_final: 0.7907 (tmm) REVERT: B 592 MET cc_start: 0.7605 (mtp) cc_final: 0.7284 (mtp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2681 time to fit residues: 27.1820 Evaluate side-chains 53 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** 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 851 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15797 Z= 0.189 Angle : 0.647 7.752 21365 Z= 0.335 Chirality : 0.043 0.155 2300 Planarity : 0.004 0.042 2761 Dihedral : 5.915 24.214 2050 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1878 helix: -0.10 (0.17), residues: 812 sheet: -1.27 (0.27), residues: 335 loop : -1.94 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 776 HIS 0.005 0.001 HIS B 157 PHE 0.018 0.002 PHE B 174 TYR 0.018 0.002 TYR A 454 ARG 0.004 0.000 ARG B 368 *********************** 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 70 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.758 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 254 MET cc_start: 0.8125 (mpp) cc_final: 0.7521 (mpp) REVERT: A 282 ASN cc_start: 0.9471 (t0) cc_final: 0.9190 (m-40) REVERT: A 744 MET cc_start: 0.7918 (tmm) cc_final: 0.7615 (tmm) REVERT: B 466 MET cc_start: 0.8257 (tmm) cc_final: 0.7946 (tmm) REVERT: B 592 MET cc_start: 0.7584 (mtp) cc_final: 0.7144 (mtp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2927 time to fit residues: 32.0621 Evaluate side-chains 54 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15797 Z= 0.196 Angle : 0.645 7.435 21365 Z= 0.331 Chirality : 0.043 0.153 2300 Planarity : 0.004 0.044 2761 Dihedral : 5.719 23.671 2050 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1878 helix: 0.10 (0.18), residues: 806 sheet: -1.19 (0.27), residues: 335 loop : -1.78 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 776 HIS 0.005 0.001 HIS B 885 PHE 0.014 0.002 PHE A 811 TYR 0.018 0.002 TYR A 454 ARG 0.010 0.001 ARG A 687 *********************** 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 68 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8229 (mpp) cc_final: 0.7642 (mpp) REVERT: A 282 ASN cc_start: 0.9444 (t0) cc_final: 0.9158 (m-40) REVERT: A 744 MET cc_start: 0.7904 (tmm) cc_final: 0.7557 (tmm) REVERT: B 466 MET cc_start: 0.8272 (tmm) cc_final: 0.7968 (tmm) REVERT: B 592 MET cc_start: 0.7595 (mtp) cc_final: 0.7134 (mtp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2951 time to fit residues: 31.4654 Evaluate side-chains 52 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 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 245 HIS ** B 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15797 Z= 0.198 Angle : 0.654 7.752 21365 Z= 0.337 Chirality : 0.043 0.200 2300 Planarity : 0.004 0.043 2761 Dihedral : 5.686 24.243 2050 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1878 helix: 0.16 (0.18), residues: 809 sheet: -1.15 (0.27), residues: 335 loop : -1.74 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 776 HIS 0.006 0.001 HIS A 681 PHE 0.016 0.002 PHE A 811 TYR 0.017 0.002 TYR A 454 ARG 0.004 0.000 ARG B 368 ********************** 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 fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8101 (mpp) cc_final: 0.7486 (mpp) REVERT: A 282 ASN cc_start: 0.9457 (t0) cc_final: 0.9171 (m-40) REVERT: A 744 MET cc_start: 0.7929 (tmm) cc_final: 0.7581 (tmm) REVERT: A 963 MET cc_start: 0.7965 (tpt) cc_final: 0.7738 (tpt) REVERT: B 466 MET cc_start: 0.8273 (tmm) cc_final: 0.7968 (tmm) REVERT: B 592 MET cc_start: 0.7421 (mtp) cc_final: 0.7022 (mtp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2784 time to fit residues: 29.6571 Evaluate side-chains 52 residues out of total 1682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 148 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 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 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.040850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.034851 restraints weight = 280350.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.035314 restraints weight = 224158.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.035608 restraints weight = 181199.075| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15797 Z= 0.185 Angle : 0.639 8.028 21365 Z= 0.328 Chirality : 0.043 0.153 2300 Planarity : 0.004 0.046 2761 Dihedral : 5.585 23.687 2050 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 1878 helix: 0.29 (0.18), residues: 802 sheet: -1.10 (0.27), residues: 335 loop : -1.63 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 776 HIS 0.005 0.001 HIS B 885 PHE 0.015 0.001 PHE A 811 TYR 0.029 0.002 TYR A 596 ARG 0.004 0.000 ARG B 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.97 seconds wall clock time: 45 minutes 19.35 seconds (2719.35 seconds total)