Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:40:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/04_2023/6b3q_7041.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.004 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 52 5.16 5 C 10128 2.51 5 N 2638 2.21 5 O 2909 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 164": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 711": "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-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15727 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7743 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 896} 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: 7665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7665 Classifications: {'peptide': 938} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 48, 'TRANS': 889} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "a" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 27} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 111 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Time building chain proxies: 8.29, per 1000 atoms: 0.53 Number of scatterers: 15727 At special positions: 0 Unit cell: (106.227, 121.249, 154.512, 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 52 16.00 O 2909 8.00 N 2638 7.00 C 10128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS a 7 " - pdb=" SG CYS a 182 " distance=2.02 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 195 " distance=2.03 Simple disulfide: pdb=" SG CYS a 181 " - pdb=" SG CYS a 186 " distance=2.04 Simple disulfide: pdb=" SG CYS b 6 " - pdb=" SG CYS b 11 " distance=2.04 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: 6.15 Conformation dependent library (CDL) restraints added in 2.5 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 11 sheets defined 43.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.686A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.928A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.501A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.523A pdb=" N LYS A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.762A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.524A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.553A pdb=" N LEU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.913A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.597A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.639A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.696A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 4.303A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 615 removed outlier: 4.453A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.663A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.780A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 677 through 689 removed outlier: 3.747A pdb=" N ARG A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.683A pdb=" N LEU A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 701' Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.545A pdb=" N ILE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 removed outlier: 3.515A pdb=" N HIS A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.805A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 4.042A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 4.037A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.679A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 893 removed outlier: 3.516A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.825A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 921 removed outlier: 3.901A pdb=" N ARG A 920 " --> pdb=" O ASN A 917 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 921 " --> pdb=" O PHE A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 921' Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 932 through 945 removed outlier: 3.750A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.971A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.913A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.683A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.818A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.692A pdb=" N ASN B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 247 removed outlier: 3.505A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.681A pdb=" N LEU B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.715A pdb=" N TYR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.626A pdb=" N LYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.546A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.648A pdb=" N LYS B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.725A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.700A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.933A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 604 through 613 removed outlier: 5.069A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 613 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.521A pdb=" N LEU B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 677 through 690 removed outlier: 3.517A pdb=" N HIS B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 682 " --> pdb=" O PRO B 678 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 708 through 714 removed outlier: 3.887A pdb=" N ALA B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 734 through 753 removed outlier: 4.025A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.764A pdb=" N LEU B 763 " --> pdb=" O PRO B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 815 removed outlier: 3.627A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 807 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 855 through 876 removed outlier: 4.414A pdb=" N SER B 861 " --> pdb=" O HIS B 857 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 862 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 893 removed outlier: 3.713A pdb=" N LEU B 889 " --> pdb=" O HIS B 885 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 890 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.607A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.515A pdb=" N LYS B 929 " --> pdb=" O VAL B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 944 removed outlier: 3.520A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.087A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.115A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 87 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 150 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 139 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.624A pdb=" N GLU A 503 " --> pdb=" O LEU A 301 " (cutoff:3.500A) 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 561 through 563 removed outlier: 6.215A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 728 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 834 removed outlier: 4.618A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 840 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 834 removed outlier: 4.618A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 793 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 990 " --> pdb=" O TRP A 776 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 778 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.517A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 148 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 304 removed outlier: 4.612A pdb=" N THR B 358 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 304 removed outlier: 3.562A pdb=" N PHE B 370 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 367 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE B 372 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 365 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.712A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 782 removed outlier: 6.325A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 836 " --> pdb=" O ARG B 847 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1803 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: 5.55 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5046 1.34 - 1.48: 3978 1.48 - 1.61: 6992 1.61 - 1.74: 0 1.74 - 1.88: 95 Bond restraints: 16111 Sorted by residual: bond pdb=" C GLN A 638 " pdb=" N PRO A 639 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 9.98e+00 bond pdb=" CB CYS b 6 " pdb=" SG CYS b 6 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.31e+00 bond pdb=" CG1 ILE B 307 " pdb=" CD1 ILE B 307 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.98e+00 bond pdb=" C GLU A 817 " pdb=" N PRO A 818 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.25e-02 6.40e+03 2.97e+00 bond pdb=" CG1 ILE A 843 " pdb=" CD1 ILE A 843 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.95e+00 ... (remaining 16106 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.36: 289 104.36 - 111.94: 7135 111.94 - 119.51: 6287 119.51 - 127.09: 7889 127.09 - 134.66: 187 Bond angle restraints: 21787 Sorted by residual: angle pdb=" C CYS b 6 " pdb=" N CYS b 7 " pdb=" CA CYS b 7 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C ASN A 222 " pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C GLN A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta sigma weight residual 120.38 126.50 -6.12 1.37e+00 5.33e-01 1.99e+01 angle pdb=" C SER A 154 " pdb=" N HIS A 155 " pdb=" CA HIS A 155 " ideal model delta sigma weight residual 121.19 127.90 -6.71 1.59e+00 3.96e-01 1.78e+01 angle pdb=" C GLN B 502 " pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 21782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 8905 15.86 - 31.72: 648 31.72 - 47.58: 174 47.58 - 63.44: 16 63.44 - 79.30: 14 Dihedral angle restraints: 9757 sinusoidal: 4071 harmonic: 5686 Sorted by residual: dihedral pdb=" CB CYS a 7 " pdb=" SG CYS a 7 " pdb=" SG CYS a 182 " pdb=" CB CYS a 182 " ideal model delta sinusoidal sigma weight residual -86.00 -11.66 -74.34 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS a 19 " pdb=" SG CYS a 19 " pdb=" SG CYS a 195 " pdb=" CB CYS a 195 " ideal model delta sinusoidal sigma weight residual -86.00 -143.04 57.04 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CA LYS A 511 " pdb=" C LYS A 511 " pdb=" N LYS A 512 " pdb=" CA LYS A 512 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 9754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1593 0.054 - 0.108: 589 0.108 - 0.161: 145 0.161 - 0.215: 19 0.215 - 0.269: 6 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CB ILE A 103 " pdb=" CA ILE A 103 " pdb=" CG1 ILE A 103 " pdb=" CG2 ILE A 103 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 733 " pdb=" CA ILE A 733 " pdb=" CG1 ILE A 733 " pdb=" CG2 ILE A 733 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE b 10 " pdb=" CA ILE b 10 " pdb=" CG1 ILE b 10 " pdb=" CG2 ILE b 10 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2349 not shown) Planarity restraints: 2815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 821 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASN B 821 " 0.077 2.00e-02 2.50e+03 pdb=" O ASN B 821 " -0.029 2.00e-02 2.50e+03 pdb=" N THR B 822 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 223 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C LYS A 223 " 0.074 2.00e-02 2.50e+03 pdb=" O LYS A 223 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR A 224 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 224 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C TYR A 224 " -0.064 2.00e-02 2.50e+03 pdb=" O TYR A 224 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 225 " 0.022 2.00e-02 2.50e+03 ... (remaining 2812 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1605 2.75 - 3.29: 14793 3.29 - 3.82: 25685 3.82 - 4.36: 29714 4.36 - 4.90: 51397 Nonbonded interactions: 123194 Sorted by model distance: nonbonded pdb=" OH TYR A 831 " pdb=" O LEU a 188 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR A 623 " pdb=" O GLY A 626 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR B 831 " pdb=" O LEU b 13 " model vdw 2.305 2.440 nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR A 55 " pdb=" OE2 GLU A 447 " model vdw 2.318 2.440 ... (remaining 123189 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 47 through 656 or (resid 657 and (name N or name CA or nam \ e C or name O or name CB )) or resid 658 through 704 or (resid 705 and (name N o \ r name CA or name C or name O or name CB )) or resid 706 through 763 or (resid 7 \ 64 through 765 and (name N or name CA or name C or name O or name CB )) or resid \ 766 through 962 or resid 990 through 1011)) selection = (chain 'B' and (resid 47 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: 1.330 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: 8.050 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.410 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.005 0.074 16111 Z= 0.342 Angle : 1.032 10.496 21787 Z= 0.550 Chirality : 0.059 0.269 2352 Planarity : 0.008 0.085 2815 Dihedral : 12.289 79.296 6069 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.00 % 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: -4.53 (0.15), residues: 1914 helix: -3.51 (0.12), residues: 745 sheet: -2.18 (0.27), residues: 320 loop : -2.71 (0.17), residues: 849 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.954 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 outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3260 time to fit residues: 171.8627 Evaluate side-chains 157 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 332 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 HIS A 762 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 332 HIS B 573 ASN B 635 ASN ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN B 783 ASN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 GLN a 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 16111 Z= 0.271 Angle : 0.705 8.714 21787 Z= 0.366 Chirality : 0.046 0.152 2352 Planarity : 0.005 0.060 2815 Dihedral : 5.676 19.803 2091 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.57 % 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: -3.01 (0.17), residues: 1914 helix: -1.72 (0.16), residues: 763 sheet: -1.78 (0.27), residues: 353 loop : -2.22 (0.19), residues: 798 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 201 average time/residue: 0.2712 time to fit residues: 83.6346 Evaluate side-chains 155 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1701 time to fit residues: 8.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.052 16111 Z= 0.419 Angle : 0.776 9.137 21787 Z= 0.400 Chirality : 0.048 0.192 2352 Planarity : 0.006 0.052 2815 Dihedral : 5.663 20.907 2091 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 2.75 % 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: -2.30 (0.18), residues: 1914 helix: -0.87 (0.18), residues: 775 sheet: -1.62 (0.26), residues: 362 loop : -2.01 (0.21), residues: 777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 15 residues processed: 181 average time/residue: 0.2733 time to fit residues: 77.9385 Evaluate side-chains 129 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1591 time to fit residues: 7.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS B 108 HIS B 134 HIS B 148 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16111 Z= 0.228 Angle : 0.623 8.884 21787 Z= 0.317 Chirality : 0.044 0.176 2352 Planarity : 0.004 0.049 2815 Dihedral : 5.208 20.135 2091 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 2.05 % 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: -1.79 (0.19), residues: 1914 helix: -0.35 (0.18), residues: 779 sheet: -1.47 (0.26), residues: 363 loop : -1.79 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 163 average time/residue: 0.2712 time to fit residues: 69.8713 Evaluate side-chains 130 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1786 time to fit residues: 6.4159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.0370 chunk 164 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16111 Z= 0.260 Angle : 0.646 12.016 21787 Z= 0.324 Chirality : 0.043 0.129 2352 Planarity : 0.004 0.047 2815 Dihedral : 5.088 20.084 2091 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 2.05 % 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: -1.57 (0.19), residues: 1914 helix: -0.08 (0.19), residues: 789 sheet: -1.40 (0.26), residues: 367 loop : -1.78 (0.22), residues: 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 11 residues processed: 163 average time/residue: 0.2674 time to fit residues: 68.1266 Evaluate side-chains 132 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1632 time to fit residues: 6.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16111 Z= 0.175 Angle : 0.598 9.705 21787 Z= 0.298 Chirality : 0.043 0.144 2352 Planarity : 0.004 0.038 2815 Dihedral : 4.882 22.962 2091 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.52 % 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: -1.24 (0.19), residues: 1914 helix: 0.22 (0.19), residues: 780 sheet: -1.21 (0.26), residues: 367 loop : -1.64 (0.22), residues: 767 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 6 residues processed: 157 average time/residue: 0.2653 time to fit residues: 65.8444 Evaluate side-chains 132 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1464 time to fit residues: 4.3567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 0.3980 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 ASN ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 16111 Z= 0.218 Angle : 0.622 15.095 21787 Z= 0.310 Chirality : 0.043 0.162 2352 Planarity : 0.004 0.045 2815 Dihedral : 4.829 24.602 2091 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.23 % 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: -1.15 (0.19), residues: 1914 helix: 0.35 (0.19), residues: 779 sheet: -1.18 (0.26), residues: 369 loop : -1.63 (0.22), residues: 766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 146 average time/residue: 0.2599 time to fit residues: 61.1371 Evaluate side-chains 126 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1743 time to fit residues: 4.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 143 optimal weight: 0.0470 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 514 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 16111 Z= 0.162 Angle : 0.601 11.325 21787 Z= 0.297 Chirality : 0.042 0.151 2352 Planarity : 0.003 0.039 2815 Dihedral : 4.672 25.638 2091 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.88 % 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: -0.93 (0.19), residues: 1914 helix: 0.51 (0.19), residues: 782 sheet: -1.03 (0.27), residues: 358 loop : -1.51 (0.22), residues: 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 146 average time/residue: 0.2654 time to fit residues: 62.3734 Evaluate side-chains 126 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1624 time to fit residues: 3.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 175 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 154 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 180 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16111 Z= 0.146 Angle : 0.601 10.857 21787 Z= 0.297 Chirality : 0.042 0.144 2352 Planarity : 0.003 0.042 2815 Dihedral : 4.563 26.688 2091 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.59 % 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: -0.74 (0.19), residues: 1914 helix: 0.65 (0.19), residues: 780 sheet: -0.94 (0.27), residues: 352 loop : -1.38 (0.22), residues: 782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 145 average time/residue: 0.2595 time to fit residues: 60.3992 Evaluate side-chains 130 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1843 time to fit residues: 4.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 294 GLN ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16111 Z= 0.227 Angle : 0.639 12.301 21787 Z= 0.318 Chirality : 0.043 0.164 2352 Planarity : 0.004 0.035 2815 Dihedral : 4.647 30.428 2091 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1914 helix: 0.61 (0.19), residues: 781 sheet: -0.95 (0.27), residues: 355 loop : -1.41 (0.22), residues: 778 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 127 average time/residue: 0.2699 time to fit residues: 55.7416 Evaluate side-chains 122 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1546 time to fit residues: 3.5789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.078972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068801 restraints weight = 57774.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070542 restraints weight = 31116.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071714 restraints weight = 19775.613| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16111 Z= 0.175 Angle : 0.633 13.543 21787 Z= 0.312 Chirality : 0.043 0.164 2352 Planarity : 0.003 0.036 2815 Dihedral : 4.585 28.023 2091 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.53 % 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: -0.72 (0.19), residues: 1914 helix: 0.66 (0.19), residues: 781 sheet: -0.91 (0.27), residues: 352 loop : -1.37 (0.22), residues: 781 =============================================================================== Job complete usr+sys time: 2802.30 seconds wall clock time: 52 minutes 19.62 seconds (3139.62 seconds total)