Starting phenix.real_space_refine on Sat Mar 16 21:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/03_2024/6b3q_7041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/03_2024/6b3q_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_7041/03_2024/6b3q_7041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/03_2024/6b3q_7041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/03_2024/6b3q_7041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3q_7041/03_2024/6b3q_7041.pdb" } resolution = 3.7 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= 0.004 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-dev-5265/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: 8.54, per 1000 atoms: 0.54 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: 4.98 Conformation dependent library (CDL) restraints added in 3.1 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: 1.82 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: 5.60 Time building geometry restraints manager: 5.53 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: 2.520 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: 7.280 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.450 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.480 ------------------------------------------------------------------------------- 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 % Allowed : 6.79 % Favored : 93.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A 776 HIS 0.013 0.002 HIS B 155 PHE 0.056 0.003 PHE A 168 TYR 0.050 0.003 TYR A 831 ARG 0.017 0.001 ARG B 477 *********************** 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 : 1.923 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: A 254 MET cc_start: 0.7615 (pmt) cc_final: 0.7305 (pmt) REVERT: A 556 MET cc_start: 0.8428 (tpp) cc_final: 0.8164 (tpp) REVERT: A 806 MET cc_start: 0.7929 (mmp) cc_final: 0.6982 (mmp) REVERT: A 872 LYS cc_start: 0.8856 (tptp) cc_final: 0.8161 (tppt) REVERT: B 150 TYR cc_start: 0.8553 (p90) cc_final: 0.8329 (p90) REVERT: B 240 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 242 LEU cc_start: 0.9026 (mm) cc_final: 0.8716 (mp) REVERT: B 495 TRP cc_start: 0.7379 (m-90) cc_final: 0.6911 (m-90) REVERT: B 553 ASP cc_start: 0.8295 (t0) cc_final: 0.7481 (p0) REVERT: B 645 ILE cc_start: 0.9064 (mt) cc_final: 0.8724 (mt) REVERT: B 648 LYS cc_start: 0.9079 (tppt) cc_final: 0.8755 (mmmt) REVERT: B 860 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7011 (tm-30) REVERT: a 196 ASN cc_start: 0.5349 (t0) cc_final: 0.5145 (t0) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3187 time to fit residues: 167.0370 Evaluate side-chains 162 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 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: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 157 HIS A 312 ASN A 332 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 HIS A 743 GLN 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 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16111 Z= 0.273 Angle : 0.696 8.123 21787 Z= 0.360 Chirality : 0.045 0.164 2352 Planarity : 0.005 0.059 2815 Dihedral : 5.574 19.648 2091 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.87 % Allowed : 12.99 % Favored : 84.14 % 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: -2.93 (0.17), residues: 1914 helix: -1.61 (0.17), residues: 769 sheet: -1.80 (0.26), residues: 366 loop : -2.18 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 776 HIS 0.016 0.001 HIS B 291 PHE 0.039 0.002 PHE B 130 TYR 0.018 0.002 TYR A 594 ARG 0.004 0.001 ARG B 920 *********************** 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 220 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.791 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 137 SER cc_start: 0.6749 (m) cc_final: 0.6445 (p) REVERT: A 254 MET cc_start: 0.7544 (pmt) cc_final: 0.7188 (pmt) REVERT: A 556 MET cc_start: 0.8459 (tpp) cc_final: 0.8226 (tpp) REVERT: B 240 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7666 (mm-30) REVERT: B 464 ILE cc_start: 0.8959 (mt) cc_final: 0.8718 (mp) REVERT: B 553 ASP cc_start: 0.8227 (t0) cc_final: 0.7681 (p0) REVERT: B 597 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8885 (mm) REVERT: B 860 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 870 MET cc_start: 0.7803 (mmm) cc_final: 0.7287 (tpt) REVERT: B 896 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8579 (mptt) REVERT: a 184 SER cc_start: 0.8402 (t) cc_final: 0.8171 (p) REVERT: a 192 GLU cc_start: 0.7231 (pm20) cc_final: 0.6632 (tp30) outliers start: 49 outliers final: 20 residues processed: 212 average time/residue: 0.2821 time to fit residues: 91.9033 Evaluate side-chains 158 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 908 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 0.0170 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16111 Z= 0.181 Angle : 0.606 7.649 21787 Z= 0.309 Chirality : 0.043 0.177 2352 Planarity : 0.004 0.052 2815 Dihedral : 5.078 19.617 2091 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.52 % Allowed : 14.28 % Favored : 83.21 % 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: -2.09 (0.18), residues: 1914 helix: -0.75 (0.18), residues: 777 sheet: -1.49 (0.27), residues: 366 loop : -1.86 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 776 HIS 0.007 0.001 HIS B 291 PHE 0.035 0.002 PHE B 130 TYR 0.014 0.001 TYR B 249 ARG 0.004 0.000 ARG B 261 *********************** 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 205 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 2.093 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: A 195 MET cc_start: 0.8694 (mmm) cc_final: 0.8388 (mmm) REVERT: A 254 MET cc_start: 0.7427 (pmt) cc_final: 0.7097 (pmt) REVERT: A 556 MET cc_start: 0.8458 (tpp) cc_final: 0.8135 (tpp) REVERT: A 577 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7938 (tt0) REVERT: A 625 TYR cc_start: 0.7919 (m-80) cc_final: 0.7702 (m-80) REVERT: B 146 HIS cc_start: 0.8294 (m-70) cc_final: 0.7432 (m170) REVERT: B 240 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 254 MET cc_start: 0.7782 (mtm) cc_final: 0.7552 (mtm) REVERT: B 502 GLN cc_start: 0.8635 (mm-40) cc_final: 0.7985 (mm-40) REVERT: B 553 ASP cc_start: 0.8204 (t0) cc_final: 0.7563 (p0) REVERT: B 643 LYS cc_start: 0.8816 (ptmt) cc_final: 0.8615 (ptmm) REVERT: B 860 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 870 MET cc_start: 0.7898 (mmm) cc_final: 0.7568 (tpt) REVERT: a 184 SER cc_start: 0.8440 (t) cc_final: 0.8149 (p) REVERT: a 193 ASN cc_start: 0.5769 (p0) cc_final: 0.5522 (p0) outliers start: 43 outliers final: 26 residues processed: 195 average time/residue: 0.2444 time to fit residues: 73.8943 Evaluate side-chains 165 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 908 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16111 Z= 0.243 Angle : 0.610 8.302 21787 Z= 0.312 Chirality : 0.043 0.150 2352 Planarity : 0.004 0.041 2815 Dihedral : 4.941 23.525 2091 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.22 % Allowed : 14.98 % Favored : 81.80 % 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: -1.64 (0.19), residues: 1914 helix: -0.24 (0.19), residues: 781 sheet: -1.41 (0.26), residues: 370 loop : -1.69 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 776 HIS 0.006 0.001 HIS B 291 PHE 0.028 0.002 PHE B 130 TYR 0.026 0.002 TYR B 325 ARG 0.003 0.001 ARG A 200 *********************** 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 198 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 143 time to evaluate : 1.883 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: 0.7504 (pmt) cc_final: 0.7223 (pmt) REVERT: A 288 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6371 (p90) REVERT: A 508 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5440 (pt0) REVERT: A 514 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: A 556 MET cc_start: 0.8441 (tpp) cc_final: 0.8155 (tpp) REVERT: A 577 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7946 (tt0) REVERT: A 638 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: B 240 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 254 MET cc_start: 0.7974 (mtm) cc_final: 0.7658 (mtm) REVERT: B 464 ILE cc_start: 0.9100 (mt) cc_final: 0.8895 (mp) REVERT: B 502 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8111 (mm-40) REVERT: B 553 ASP cc_start: 0.8203 (t0) cc_final: 0.7748 (p0) REVERT: B 768 GLU cc_start: 0.7580 (tp30) cc_final: 0.7376 (tp30) REVERT: a 184 SER cc_start: 0.8528 (t) cc_final: 0.8141 (p) outliers start: 55 outliers final: 29 residues processed: 187 average time/residue: 0.2459 time to fit residues: 72.5648 Evaluate side-chains 160 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 908 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 164 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 overall best weight: 1.4344 ------------------------------------------------------------------------------- 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 108 HIS B 148 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16111 Z= 0.234 Angle : 0.608 12.885 21787 Z= 0.306 Chirality : 0.043 0.164 2352 Planarity : 0.004 0.039 2815 Dihedral : 4.840 21.907 2091 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.98 % Allowed : 16.56 % Favored : 80.46 % 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: -1.31 (0.19), residues: 1914 helix: 0.06 (0.19), residues: 783 sheet: -1.28 (0.26), residues: 366 loop : -1.53 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 776 HIS 0.005 0.001 HIS A 155 PHE 0.026 0.002 PHE B 130 TYR 0.029 0.001 TYR B 150 ARG 0.005 0.000 ARG B 261 *********************** 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 192 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 2.098 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: 0.7482 (pmt) cc_final: 0.7258 (pmt) REVERT: A 288 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6705 (p90) REVERT: A 508 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5348 (pt0) REVERT: A 511 LYS cc_start: 0.8475 (mmtm) cc_final: 0.8162 (mmmt) REVERT: A 556 MET cc_start: 0.8381 (tpp) cc_final: 0.8125 (tpp) REVERT: A 577 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7959 (tt0) REVERT: A 638 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: B 240 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 248 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6515 (t80) REVERT: B 254 MET cc_start: 0.8010 (mtm) cc_final: 0.7727 (mtm) REVERT: B 502 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8104 (mm-40) REVERT: B 553 ASP cc_start: 0.8189 (t0) cc_final: 0.7870 (p0) REVERT: B 768 GLU cc_start: 0.7643 (tp30) cc_final: 0.6904 (tp30) REVERT: B 860 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8073 (tm-30) REVERT: a 184 SER cc_start: 0.8645 (t) cc_final: 0.8215 (m) REVERT: a 191 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (tt) outliers start: 51 outliers final: 35 residues processed: 182 average time/residue: 0.2666 time to fit residues: 75.4556 Evaluate side-chains 171 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain a residue 191 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16111 Z= 0.238 Angle : 0.615 13.813 21787 Z= 0.307 Chirality : 0.043 0.137 2352 Planarity : 0.004 0.039 2815 Dihedral : 4.801 21.806 2091 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.39 % Allowed : 16.79 % Favored : 79.81 % 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: -1.20 (0.19), residues: 1914 helix: 0.19 (0.19), residues: 783 sheet: -1.29 (0.26), residues: 369 loop : -1.48 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.005 0.001 HIS B 730 PHE 0.029 0.002 PHE B 215 TYR 0.019 0.001 TYR B 325 ARG 0.005 0.000 ARG B 687 *********************** 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 193 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 135 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8712 (mt) REVERT: A 195 MET cc_start: 0.8775 (mmm) cc_final: 0.8355 (mmm) REVERT: A 254 MET cc_start: 0.7446 (pmt) cc_final: 0.7243 (pmt) REVERT: A 288 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6354 (p90) REVERT: A 511 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8210 (mmmt) REVERT: A 556 MET cc_start: 0.8327 (tpp) cc_final: 0.8067 (tpp) REVERT: A 577 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7954 (tt0) REVERT: A 638 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: B 248 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6770 (t80) REVERT: B 249 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6182 (t80) REVERT: B 254 MET cc_start: 0.8108 (mtm) cc_final: 0.7747 (mtm) REVERT: B 431 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7280 (ttt180) REVERT: B 464 ILE cc_start: 0.9135 (mt) cc_final: 0.8929 (mp) REVERT: B 502 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8052 (mm-40) REVERT: B 553 ASP cc_start: 0.8187 (t0) cc_final: 0.7878 (p0) REVERT: a 191 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8671 (tt) outliers start: 58 outliers final: 39 residues processed: 183 average time/residue: 0.2480 time to fit residues: 72.1706 Evaluate side-chains 173 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain a residue 191 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** 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: 0.8116 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 : 0.005 0.042 16111 Z= 0.301 Angle : 0.649 11.409 21787 Z= 0.326 Chirality : 0.044 0.141 2352 Planarity : 0.004 0.035 2815 Dihedral : 4.914 22.558 2091 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.45 % Allowed : 17.55 % Favored : 78.99 % 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: -1.23 (0.19), residues: 1914 helix: 0.26 (0.19), residues: 781 sheet: -1.25 (0.26), residues: 359 loop : -1.64 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 355 HIS 0.006 0.001 HIS B 730 PHE 0.027 0.002 PHE B 215 TYR 0.020 0.002 TYR B 628 ARG 0.004 0.001 ARG A 767 *********************** 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 191 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 132 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8765 (mmm) cc_final: 0.8311 (mmm) REVERT: A 288 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6216 (p90) REVERT: A 508 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5532 (pt0) REVERT: A 556 MET cc_start: 0.8313 (tpp) cc_final: 0.8087 (tpp) REVERT: A 577 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7977 (tt0) REVERT: A 638 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: B 189 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 248 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 249 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6273 (t80) REVERT: B 254 MET cc_start: 0.8162 (mtm) cc_final: 0.7793 (mtm) REVERT: B 431 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7280 (ttt180) REVERT: B 464 ILE cc_start: 0.9109 (mt) cc_final: 0.8904 (mp) REVERT: B 502 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8038 (mm-40) REVERT: B 553 ASP cc_start: 0.8194 (t0) cc_final: 0.7934 (p0) REVERT: B 844 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: B 860 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 908 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.8139 (t-100) REVERT: a 191 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8736 (tt) outliers start: 59 outliers final: 38 residues processed: 181 average time/residue: 0.2604 time to fit residues: 73.8093 Evaluate side-chains 168 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 844 GLN Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 908 TRP Chi-restraints excluded: chain a residue 3 ASN Chi-restraints excluded: chain a residue 191 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS ** B 148 ASN ** 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 573 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: 0.8085 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16111 Z= 0.203 Angle : 0.612 12.368 21787 Z= 0.306 Chirality : 0.043 0.145 2352 Planarity : 0.004 0.037 2815 Dihedral : 4.794 21.357 2091 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.51 % Allowed : 17.96 % Favored : 78.53 % 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: -1.02 (0.19), residues: 1914 helix: 0.43 (0.19), residues: 776 sheet: -1.14 (0.26), residues: 352 loop : -1.51 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 495 HIS 0.006 0.001 HIS B 589 PHE 0.039 0.002 PHE A 109 TYR 0.021 0.001 TYR B 628 ARG 0.004 0.000 ARG B 839 *********************** 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 196 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (mt) REVERT: A 288 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6126 (p90) REVERT: A 511 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7966 (mmmt) REVERT: A 556 MET cc_start: 0.8340 (tpp) cc_final: 0.8115 (tpp) REVERT: A 577 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7948 (tt0) REVERT: A 638 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: B 189 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 248 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 249 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6136 (t80) REVERT: B 254 MET cc_start: 0.8115 (mtm) cc_final: 0.7729 (mtm) REVERT: B 303 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7729 (mttt) REVERT: B 431 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7297 (ttt180) REVERT: B 464 ILE cc_start: 0.9125 (mt) cc_final: 0.8913 (mp) REVERT: B 502 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8022 (mm-40) REVERT: B 553 ASP cc_start: 0.8176 (t0) cc_final: 0.7941 (p0) REVERT: B 625 TYR cc_start: 0.7946 (m-10) cc_final: 0.7492 (m-10) REVERT: B 839 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7706 (mmt90) REVERT: B 844 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: B 860 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8031 (tm-30) REVERT: a 191 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8731 (tt) outliers start: 60 outliers final: 39 residues processed: 184 average time/residue: 0.2477 time to fit residues: 71.6657 Evaluate side-chains 175 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 844 GLN Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain a residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16111 Z= 0.160 Angle : 0.595 12.041 21787 Z= 0.294 Chirality : 0.042 0.138 2352 Planarity : 0.003 0.038 2815 Dihedral : 4.569 19.420 2091 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.75 % Allowed : 18.49 % Favored : 78.76 % 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: -0.78 (0.19), residues: 1914 helix: 0.66 (0.19), residues: 776 sheet: -1.01 (0.26), residues: 345 loop : -1.42 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 495 HIS 0.005 0.001 HIS B 332 PHE 0.034 0.001 PHE B 215 TYR 0.022 0.001 TYR B 628 ARG 0.004 0.000 ARG B 839 *********************** 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 194 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.970 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: A 288 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6381 (p90) REVERT: A 508 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5368 (pt0) REVERT: A 511 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8007 (mmmt) REVERT: A 556 MET cc_start: 0.8280 (tpp) cc_final: 0.8073 (tpp) REVERT: A 577 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7886 (tt0) REVERT: A 612 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 638 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: B 248 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6792 (t80) REVERT: B 249 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6045 (t80) REVERT: B 254 MET cc_start: 0.7884 (mtm) cc_final: 0.7478 (mtm) REVERT: B 303 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7691 (mttt) REVERT: B 464 ILE cc_start: 0.9029 (mt) cc_final: 0.8818 (mp) REVERT: B 502 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 776 TRP cc_start: 0.6221 (t60) cc_final: 0.6019 (t60) REVERT: B 839 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7873 (mmt90) REVERT: B 844 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: B 860 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8019 (tm-30) outliers start: 47 outliers final: 36 residues processed: 185 average time/residue: 0.2453 time to fit residues: 71.8126 Evaluate side-chains 180 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 844 GLN Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain b residue 10 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** 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: 0.8070 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16111 Z= 0.195 Angle : 0.620 11.082 21787 Z= 0.309 Chirality : 0.043 0.165 2352 Planarity : 0.004 0.036 2815 Dihedral : 4.561 19.402 2091 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.87 % Allowed : 18.90 % Favored : 78.23 % 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: -0.69 (0.19), residues: 1914 helix: 0.75 (0.19), residues: 775 sheet: -0.99 (0.27), residues: 345 loop : -1.37 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 495 HIS 0.004 0.001 HIS B 332 PHE 0.033 0.001 PHE B 215 TYR 0.021 0.001 TYR B 628 ARG 0.004 0.000 ARG B 839 ********************** 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 184 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6377 (p90) REVERT: A 508 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.4916 (pt0) REVERT: A 511 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8050 (mmmt) REVERT: A 556 MET cc_start: 0.8328 (tpp) cc_final: 0.8069 (tpp) REVERT: A 577 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7887 (tt0) REVERT: A 638 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: B 248 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6901 (t80) REVERT: B 249 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6043 (t80) REVERT: B 254 MET cc_start: 0.8055 (mtm) cc_final: 0.7654 (mtm) REVERT: B 303 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7688 (mttt) REVERT: B 426 ASP cc_start: 0.7424 (t70) cc_final: 0.7224 (p0) REVERT: B 464 ILE cc_start: 0.9050 (mt) cc_final: 0.8836 (mp) REVERT: B 839 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7911 (mmt90) REVERT: B 844 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: B 860 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8039 (tm-30) outliers start: 49 outliers final: 40 residues processed: 173 average time/residue: 0.2469 time to fit residues: 68.6009 Evaluate side-chains 176 residues out of total 1722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 638 GLN Chi-restraints excluded: chain A residue 649 MET Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 844 GLN Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 867 LEU 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: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 GLN B 148 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068316 restraints weight = 57783.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070021 restraints weight = 31127.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071198 restraints weight = 19856.299| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4886 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= 0.191 Angle : 0.619 11.142 21787 Z= 0.308 Chirality : 0.043 0.160 2352 Planarity : 0.004 0.037 2815 Dihedral : 4.550 19.260 2091 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.87 % Allowed : 19.19 % Favored : 77.94 % 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: -0.64 (0.19), residues: 1914 helix: 0.79 (0.19), residues: 774 sheet: -0.95 (0.27), residues: 343 loop : -1.33 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 495 HIS 0.005 0.001 HIS B 589 PHE 0.033 0.001 PHE B 215 TYR 0.021 0.001 TYR B 628 ARG 0.004 0.000 ARG B 839 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.82 seconds wall clock time: 54 minutes 58.07 seconds (3298.07 seconds total)