Starting phenix.real_space_refine on Sun Mar 24 20:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bst_30166/03_2024/7bst_30166.pdb" } resolution = 4.37 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15738 atoms to isotropic. 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 64 5.16 5 C 18012 2.51 5 N 4729 2.21 5 O 5461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 916": "NH1" <-> "NH2" Residue "B ARG 989": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 989": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28266 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7906 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 10, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 943} Chain breaks: 5 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 13, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 956} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3732 Classifications: {'peptide': 472} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 440} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3735 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "G" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Time building chain proxies: 14.06, per 1000 atoms: 0.50 Number of scatterers: 28266 At special positions: 0 Unit cell: (129.6, 184.95, 162, 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 64 16.00 O 5461 8.00 N 4729 7.00 C 18012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.52 Conformation dependent library (CDL) restraints added in 4.5 seconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 22 sheets defined 47.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'B' and resid 32 through 48 Processing helix chain 'B' and resid 56 through 73 removed outlier: 3.946A pdb=" N MET B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.590A pdb=" N ILE B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.609A pdb=" N ASN B 132 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.895A pdb=" N PHE B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 248 removed outlier: 3.514A pdb=" N PHE B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 removed outlier: 3.536A pdb=" N TYR B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 293 removed outlier: 3.698A pdb=" N GLU B 281 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.861A pdb=" N GLU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 removed outlier: 3.529A pdb=" N GLU B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.825A pdb=" N ASN B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.745A pdb=" N TYR B 399 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.705A pdb=" N GLN B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.978A pdb=" N ALA B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.823A pdb=" N SER B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.506A pdb=" N GLU B 515 " --> pdb=" O MET B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 564 removed outlier: 3.852A pdb=" N THR B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 620 Processing helix chain 'B' and resid 632 through 647 Processing helix chain 'B' and resid 678 through 687 Processing helix chain 'B' and resid 708 through 718 Processing helix chain 'B' and resid 723 through 728 removed outlier: 4.050A pdb=" N VAL B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 removed outlier: 3.717A pdb=" N MET B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 763 removed outlier: 3.771A pdb=" N VAL B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 769 Processing helix chain 'B' and resid 771 through 793 removed outlier: 3.595A pdb=" N PHE B 778 " --> pdb=" O GLU B 774 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 removed outlier: 3.994A pdb=" N ALA B 799 " --> pdb=" O TYR B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 removed outlier: 4.499A pdb=" N PHE B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 835 removed outlier: 3.778A pdb=" N GLN B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 858 removed outlier: 3.568A pdb=" N ARG B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 900 removed outlier: 3.557A pdb=" N PHE B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 919 removed outlier: 3.742A pdb=" N ARG B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 938 removed outlier: 3.810A pdb=" N VAL B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 971 removed outlier: 3.514A pdb=" N ILE B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 966 " --> pdb=" O GLN B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 975 through 990 removed outlier: 3.645A pdb=" N ARG B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'C' and resid 32 through 48 removed outlier: 3.556A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 72 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.892A pdb=" N ASN C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.740A pdb=" N LYS C 196 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 198 " --> pdb=" O PHE C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.590A pdb=" N SER C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 273 through 294 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 313 through 326 removed outlier: 3.530A pdb=" N SER C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.525A pdb=" N GLN C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.535A pdb=" N TYR C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 414 removed outlier: 4.489A pdb=" N GLN C 414 " --> pdb=" O HIS C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 414' Processing helix chain 'C' and resid 415 through 425 removed outlier: 3.696A pdb=" N GLN C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 486 through 491 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'C' and resid 509 through 528 removed outlier: 3.551A pdb=" N TYR C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 569 removed outlier: 3.691A pdb=" N ALA C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 568 " --> pdb=" O ALA C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 623 Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 680 through 687 Processing helix chain 'C' and resid 708 through 720 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 752 through 763 removed outlier: 3.547A pdb=" N ARG C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 793 removed outlier: 4.176A pdb=" N GLU C 784 " --> pdb=" O LYS C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 804 Processing helix chain 'C' and resid 805 through 807 No H-bonds generated for 'chain 'C' and resid 805 through 807' Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 825 through 835 removed outlier: 3.509A pdb=" N ILE C 835 " --> pdb=" O GLU C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 857 Processing helix chain 'C' and resid 890 through 898 Processing helix chain 'C' and resid 913 through 921 removed outlier: 3.927A pdb=" N LEU C 917 " --> pdb=" O GLU C 913 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 921 " --> pdb=" O LEU C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 938 removed outlier: 3.659A pdb=" N VAL C 931 " --> pdb=" O LYS C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 943 Processing helix chain 'C' and resid 945 through 971 removed outlier: 4.018A pdb=" N ILE C 949 " --> pdb=" O ASP C 945 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 989 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.994A pdb=" N ILE D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 53 removed outlier: 3.847A pdb=" N PHE D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 34 " --> pdb=" O TRP D 30 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR D 35 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 146 through 163 Processing helix chain 'D' and resid 178 through 185 Processing helix chain 'D' and resid 185 through 190 removed outlier: 4.422A pdb=" N ALA D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.690A pdb=" N LEU D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 removed outlier: 3.994A pdb=" N ASN D 271 " --> pdb=" O PHE D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 271' Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.654A pdb=" N ALA D 324 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.847A pdb=" N VAL D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 344 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.706A pdb=" N GLU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 378 " --> pdb=" O TYR D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.965A pdb=" N ILE D 439 " --> pdb=" O HIS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 4.063A pdb=" N LEU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 489 " --> pdb=" O ILE D 485 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 499 " --> pdb=" O THR D 495 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 22 removed outlier: 3.570A pdb=" N ILE E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 54 removed outlier: 4.322A pdb=" N PHE E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN E 34 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR E 35 " --> pdb=" O ASP E 31 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER E 50 " --> pdb=" O SER E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 115 through 121 Processing helix chain 'E' and resid 146 through 163 removed outlier: 3.792A pdb=" N LYS E 150 " --> pdb=" O THR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 177 removed outlier: 3.584A pdb=" N PHE E 177 " --> pdb=" O ILE E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 177' Processing helix chain 'E' and resid 178 through 186 removed outlier: 3.876A pdb=" N PHE E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.832A pdb=" N GLN E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.816A pdb=" N MET E 267 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE E 268 " --> pdb=" O ARG E 264 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 270 " --> pdb=" O ASN E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 removed outlier: 4.148A pdb=" N ILE E 318 " --> pdb=" O PRO E 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP E 320 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 344 removed outlier: 4.123A pdb=" N PHE E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 340 " --> pdb=" O ASP E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 376 removed outlier: 4.208A pdb=" N LYS E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE E 371 " --> pdb=" O ALA E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 445 removed outlier: 3.881A pdb=" N ILE E 439 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 507 removed outlier: 3.677A pdb=" N LEU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN E 489 " --> pdb=" O ILE E 485 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 499 " --> pdb=" O THR E 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 24 removed outlier: 3.682A pdb=" N VAL F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 48 through 58 removed outlier: 3.811A pdb=" N VAL F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 76 through 105 removed outlier: 4.569A pdb=" N ASN F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.682A pdb=" N VAL G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 48 through 58 removed outlier: 3.811A pdb=" N VAL G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 105 removed outlier: 4.569A pdb=" N ASN G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.803A pdb=" N ASN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.407A pdb=" N PHE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 157 through 190 removed outlier: 4.316A pdb=" N ILE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.886A pdb=" N VAL A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.629A pdb=" N ILE A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.537A pdb=" N LEU A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.836A pdb=" N GLN A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 removed outlier: 4.026A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.600A pdb=" N GLU B 50 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 152 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 154 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N LEU B 200 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 161 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL B 202 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 163 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER B 204 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 165 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AA3, first strand: chain 'B' and resid 229 through 230 removed outlier: 4.234A pdb=" N TRP B 229 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AA5, first strand: chain 'B' and resid 378 through 381 removed outlier: 4.253A pdb=" N ASP B 408 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 381 removed outlier: 4.253A pdb=" N ASP B 408 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE B 434 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE B 407 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR B 304 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS B 459 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 474 through 477 removed outlier: 6.929A pdb=" N LYS B 474 " --> pdb=" O GLY B 700 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 702 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS B 476 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B 704 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN B 669 " --> pdb=" O PHE B 699 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN B 539 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR B 670 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 541 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 672 " --> pdb=" O MET B 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 576 through 578 removed outlier: 3.507A pdb=" N ILE B 654 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 138 removed outlier: 3.686A pdb=" N VAL C 162 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 156 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 204 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 264 removed outlier: 3.524A pdb=" N THR C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.624A pdb=" N THR C 381 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 403 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE C 432 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE C 405 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE C 434 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 407 " --> pdb=" O PHE C 434 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR C 304 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER C 460 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP C 306 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 477 through 479 removed outlier: 6.770A pdb=" N ASN C 669 " --> pdb=" O ASN C 701 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL C 703 " --> pdb=" O ASN C 669 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C 671 " --> pdb=" O VAL C 703 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN C 539 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C 670 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 541 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 672 " --> pdb=" O MET C 541 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 540 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 655 " --> pdb=" O ALA C 540 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU C 542 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA C 577 " --> pdb=" O ILE C 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 224 through 226 removed outlier: 6.850A pdb=" N GLY D 252 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.566A pdb=" N ILE D 299 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA D 354 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER D 405 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL D 381 " --> pdb=" O SER D 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 251 through 254 Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 357 Processing sheet with id=AB9, first strand: chain 'A' and resid 17 through 20 Processing sheet with id=AC1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.850A pdb=" N LYS A 99 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 202 through 205 removed outlier: 3.998A pdb=" N GLU A 202 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 249 through 251 removed outlier: 4.477A pdb=" N ASP A 249 " --> pdb=" O TRP A 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 284 through 287 removed outlier: 3.942A pdb=" N ALA A 285 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 270 " --> pdb=" O ALA A 285 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 3189 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: 9.08 Time building geometry restraints manager: 11.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9033 1.34 - 1.46: 6295 1.46 - 1.58: 13375 1.58 - 1.70: 0 1.70 - 1.83: 116 Bond restraints: 28819 Sorted by residual: bond pdb=" N LEU B1009 " pdb=" CA LEU B1009 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.90e-02 2.77e+03 6.02e+00 bond pdb=" C ASP D 314 " pdb=" N PRO D 315 " ideal model delta sigma weight residual 1.334 1.388 -0.055 2.34e-02 1.83e+03 5.43e+00 bond pdb=" C ASP E 314 " pdb=" N PRO E 315 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.40e+00 bond pdb=" C ASN C1010 " pdb=" N PRO C1011 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.72e+00 bond pdb=" C THR D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.331 1.357 -0.025 1.21e-02 6.83e+03 4.37e+00 ... (remaining 28814 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.32: 541 106.32 - 113.82: 15887 113.82 - 121.32: 15217 121.32 - 128.82: 7132 128.82 - 136.31: 167 Bond angle restraints: 38944 Sorted by residual: angle pdb=" C PRO B1008 " pdb=" N LEU B1009 " pdb=" CA LEU B1009 " ideal model delta sigma weight residual 121.70 134.68 -12.98 1.80e+00 3.09e-01 5.20e+01 angle pdb=" C GLY A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.06 128.16 -8.10 1.19e+00 7.06e-01 4.63e+01 angle pdb=" C GLU B 860 " pdb=" N LYS B 861 " pdb=" CA LYS B 861 " ideal model delta sigma weight residual 121.70 133.42 -11.72 1.80e+00 3.09e-01 4.24e+01 angle pdb=" C GLU E 420 " pdb=" N LEU E 421 " pdb=" CA LEU E 421 " ideal model delta sigma weight residual 121.70 132.22 -10.52 1.80e+00 3.09e-01 3.42e+01 angle pdb=" C LEU B1003 " pdb=" N PRO B1004 " pdb=" CD PRO B1004 " ideal model delta sigma weight residual 120.60 107.87 12.73 2.20e+00 2.07e-01 3.35e+01 ... (remaining 38939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 16262 16.10 - 32.21: 857 32.21 - 48.31: 205 48.31 - 64.41: 10 64.41 - 80.52: 25 Dihedral angle restraints: 17359 sinusoidal: 7002 harmonic: 10357 Sorted by residual: dihedral pdb=" CA VAL E 474 " pdb=" C VAL E 474 " pdb=" N GLU E 475 " pdb=" CA GLU E 475 " ideal model delta harmonic sigma weight residual 180.00 137.51 42.49 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA ARG C 678 " pdb=" C ARG C 678 " pdb=" N TYR C 679 " pdb=" CA TYR C 679 " ideal model delta harmonic sigma weight residual -180.00 -140.44 -39.56 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA TYR E 274 " pdb=" C TYR E 274 " pdb=" N ASP E 275 " pdb=" CA ASP E 275 " ideal model delta harmonic sigma weight residual -180.00 -142.84 -37.16 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 17356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3627 0.076 - 0.151: 611 0.151 - 0.227: 57 0.227 - 0.303: 10 0.303 - 0.379: 2 Chirality restraints: 4307 Sorted by residual: chirality pdb=" CB ILE D 79 " pdb=" CA ILE D 79 " pdb=" CG1 ILE D 79 " pdb=" CG2 ILE D 79 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB VAL D 27 " pdb=" CA VAL D 27 " pdb=" CG1 VAL D 27 " pdb=" CG2 VAL D 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4304 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 302 " 0.058 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO E 303 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 303 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 303 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 17 " 0.032 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP E 17 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP E 17 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 17 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 17 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 17 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 17 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 17 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.027 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP A 117 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " -0.002 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4717 2.77 - 3.30: 27085 3.30 - 3.83: 46837 3.83 - 4.37: 54373 4.37 - 4.90: 88716 Nonbonded interactions: 221728 Sorted by model distance: nonbonded pdb=" O GLY E 131 " pdb=" OH TYR E 274 " model vdw 2.232 2.440 nonbonded pdb=" O ILE B 713 " pdb=" OG1 THR B 717 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR E 411 " pdb=" O VAL E 456 " model vdw 2.277 2.440 nonbonded pdb=" OG SER C 581 " pdb=" O THR C 598 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR G 7 " pdb=" OD2 ASP G 92 " model vdw 2.287 2.440 ... (remaining 221723 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 'B' and (resid 30 through 180 or resid 191 through 861 or resid 872 throu \ gh 1035)) selection = (chain 'C' and (resid 30 through 584 or resid 591 through 1035)) } ncs_group { reference = (chain 'D' and (resid 10 through 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 510)) selection = (chain 'E' and (resid 10 through 55 or resid 72 through 510)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.020 Extract box with map and model: 4.960 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 68.600 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.004 0.069 28819 Z= 0.287 Angle : 1.029 17.895 38944 Z= 0.563 Chirality : 0.056 0.379 4307 Planarity : 0.007 0.088 5056 Dihedral : 11.111 80.515 10637 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.56 % Allowed : 4.01 % Favored : 95.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 2.17 % Twisted General : 0.29 % 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: -4.41 (0.11), residues: 3464 helix: -2.73 (0.10), residues: 1505 sheet: -2.27 (0.29), residues: 264 loop : -3.23 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP E 17 HIS 0.014 0.002 HIS A 313 PHE 0.030 0.003 PHE C 954 TYR 0.056 0.003 TYR B 846 ARG 0.021 0.001 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 432 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.7190 (mmm) cc_final: 0.6744 (mmm) REVERT: B 390 MET cc_start: 0.7724 (mtm) cc_final: 0.7479 (mtt) REVERT: B 786 LEU cc_start: 0.9440 (mt) cc_final: 0.9213 (tt) REVERT: B 997 THR cc_start: 0.8549 (p) cc_final: 0.8298 (t) REVERT: C 155 LEU cc_start: 0.9278 (mt) cc_final: 0.8923 (mt) REVERT: C 335 PHE cc_start: 0.7848 (t80) cc_final: 0.7360 (t80) REVERT: C 652 LEU cc_start: 0.9093 (tp) cc_final: 0.8655 (mp) REVERT: C 737 MET cc_start: 0.8127 (mmm) cc_final: 0.7454 (mmm) REVERT: C 752 PHE cc_start: 0.8232 (t80) cc_final: 0.7126 (t80) REVERT: C 753 MET cc_start: 0.7937 (mmm) cc_final: 0.7667 (mmt) REVERT: D 206 SER cc_start: 0.9316 (m) cc_final: 0.8695 (p) REVERT: E 157 VAL cc_start: 0.7409 (t) cc_final: 0.7177 (p) REVERT: E 291 ARG cc_start: 0.7788 (mpp80) cc_final: 0.7436 (tpm170) REVERT: E 319 ASN cc_start: 0.8312 (t0) cc_final: 0.7506 (p0) REVERT: E 431 LEU cc_start: 0.7693 (mt) cc_final: 0.7412 (mp) REVERT: F 21 ASN cc_start: 0.8928 (m-40) cc_final: 0.7903 (p0) REVERT: F 87 GLU cc_start: 0.9065 (tt0) cc_final: 0.8649 (tp30) REVERT: F 89 LEU cc_start: 0.9465 (mt) cc_final: 0.8972 (pp) REVERT: G 17 MET cc_start: 0.8610 (mtp) cc_final: 0.8373 (mtt) REVERT: G 21 ASN cc_start: 0.8396 (m-40) cc_final: 0.7833 (p0) REVERT: G 65 PHE cc_start: 0.7329 (m-10) cc_final: 0.6528 (m-10) REVERT: A 100 MET cc_start: 0.5845 (mmm) cc_final: 0.5268 (tmm) REVERT: A 217 THR cc_start: 0.4746 (m) cc_final: 0.4015 (t) REVERT: A 380 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6648 (pp20) outliers start: 17 outliers final: 2 residues processed: 448 average time/residue: 0.4566 time to fit residues: 304.9911 Evaluate side-chains 199 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.9980 chunk 263 optimal weight: 0.0670 chunk 146 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 316 optimal weight: 6.9990 overall best weight: 1.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 69 GLN B 91 ASN B 199 GLN B 221 ASN B 267 GLN B 370 ASN B 376 ASN B 388 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 622 HIS B 924 ASN C 46 ASN ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 70 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 459 HIS ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS C 701 ASN C 726 ASN C 958 GLN ** C 995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN D 90 GLN D 302 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN D 412 ASN D 414 GLN D 427 ASN D 489 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN E 100 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN E 435 HIS E 467 ASN E 489 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN A 119 ASN A 313 HIS ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28819 Z= 0.212 Angle : 0.701 15.911 38944 Z= 0.371 Chirality : 0.045 0.227 4307 Planarity : 0.005 0.068 5056 Dihedral : 6.887 36.623 3789 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.13), residues: 3464 helix: -1.16 (0.12), residues: 1527 sheet: -1.80 (0.30), residues: 290 loop : -2.95 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 117 HIS 0.008 0.001 HIS F 34 PHE 0.042 0.002 PHE D 277 TYR 0.026 0.002 TYR D 260 ARG 0.013 0.001 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 MET cc_start: 0.7398 (mmm) cc_final: 0.6953 (mmm) REVERT: B 390 MET cc_start: 0.7474 (mtm) cc_final: 0.7233 (ptm) REVERT: B 686 PHE cc_start: 0.9025 (m-10) cc_final: 0.8599 (m-80) REVERT: C 44 LEU cc_start: 0.8540 (mt) cc_final: 0.8340 (mt) REVERT: C 227 MET cc_start: 0.6399 (mmp) cc_final: 0.5875 (mmm) REVERT: C 335 PHE cc_start: 0.7957 (t80) cc_final: 0.7507 (t80) REVERT: C 390 MET cc_start: 0.8011 (tpp) cc_final: 0.7606 (tpp) REVERT: C 652 LEU cc_start: 0.9015 (tp) cc_final: 0.8753 (mp) REVERT: C 653 LEU cc_start: 0.8726 (tt) cc_final: 0.8487 (tt) REVERT: D 139 THR cc_start: 0.8748 (p) cc_final: 0.8482 (t) REVERT: D 265 MET cc_start: 0.8076 (ptp) cc_final: 0.7771 (ptm) REVERT: D 393 PHE cc_start: 0.5581 (t80) cc_final: 0.5161 (t80) REVERT: E 291 ARG cc_start: 0.8011 (mpp80) cc_final: 0.7473 (tpm170) REVERT: E 431 LEU cc_start: 0.7681 (mt) cc_final: 0.7424 (pt) REVERT: F 21 ASN cc_start: 0.8657 (m-40) cc_final: 0.7486 (m110) REVERT: F 71 MET cc_start: 0.6546 (ptt) cc_final: 0.6132 (ppp) REVERT: F 93 LEU cc_start: 0.8653 (mt) cc_final: 0.8390 (mt) REVERT: G 17 MET cc_start: 0.8520 (mtp) cc_final: 0.8238 (mtt) REVERT: G 21 ASN cc_start: 0.8584 (m-40) cc_final: 0.8239 (p0) REVERT: G 65 PHE cc_start: 0.6345 (m-10) cc_final: 0.6061 (m-10) REVERT: A 98 MET cc_start: -0.2448 (ttm) cc_final: -0.2955 (ttm) REVERT: A 100 MET cc_start: 0.6301 (mmm) cc_final: 0.5497 (tmm) outliers start: 5 outliers final: 0 residues processed: 262 average time/residue: 0.4208 time to fit residues: 173.5121 Evaluate side-chains 154 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 316 optimal weight: 30.0000 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 313 optimal weight: 0.0060 chunk 107 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN B 370 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN C 57 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN E 203 GLN E 211 GLN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28819 Z= 0.199 Angle : 0.671 14.998 38944 Z= 0.352 Chirality : 0.044 0.201 4307 Planarity : 0.005 0.065 5056 Dihedral : 6.453 33.579 3789 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.38 (0.14), residues: 3464 helix: -0.41 (0.13), residues: 1522 sheet: -1.61 (0.30), residues: 300 loop : -2.79 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 17 HIS 0.007 0.001 HIS F 34 PHE 0.034 0.001 PHE D 277 TYR 0.035 0.002 TYR D 260 ARG 0.010 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7686 (mpp) cc_final: 0.7314 (mmt) REVERT: B 130 MET cc_start: 0.7402 (mmm) cc_final: 0.6964 (mmm) REVERT: B 422 LEU cc_start: 0.8789 (mt) cc_final: 0.8552 (mt) REVERT: B 686 PHE cc_start: 0.9031 (m-10) cc_final: 0.8790 (m-80) REVERT: C 155 LEU cc_start: 0.9360 (mp) cc_final: 0.8849 (mt) REVERT: C 348 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8401 (mmmt) REVERT: C 542 LEU cc_start: 0.8950 (mt) cc_final: 0.8735 (mt) REVERT: C 653 LEU cc_start: 0.8743 (tt) cc_final: 0.8507 (tt) REVERT: C 910 MET cc_start: 0.7359 (mmp) cc_final: 0.6462 (mmm) REVERT: D 93 CYS cc_start: 0.6831 (t) cc_final: 0.6518 (t) REVERT: D 393 PHE cc_start: 0.5658 (t80) cc_final: 0.5371 (t80) REVERT: D 468 LEU cc_start: 0.7266 (tp) cc_final: 0.7046 (tp) REVERT: E 265 MET cc_start: 0.8933 (pmm) cc_final: 0.8246 (pmm) REVERT: E 291 ARG cc_start: 0.8024 (mpp80) cc_final: 0.7398 (tpm170) REVERT: E 319 ASN cc_start: 0.8509 (m-40) cc_final: 0.8236 (m-40) REVERT: E 431 LEU cc_start: 0.7566 (mt) cc_final: 0.7299 (pt) REVERT: F 71 MET cc_start: 0.6794 (ptt) cc_final: 0.5946 (ppp) REVERT: F 89 LEU cc_start: 0.9228 (mm) cc_final: 0.9015 (mm) REVERT: F 93 LEU cc_start: 0.8767 (mt) cc_final: 0.8530 (mt) REVERT: G 17 MET cc_start: 0.8454 (mtp) cc_final: 0.8242 (mtt) REVERT: G 21 ASN cc_start: 0.8712 (m-40) cc_final: 0.8078 (m110) REVERT: G 96 ASP cc_start: 0.7784 (m-30) cc_final: 0.7504 (m-30) REVERT: A 100 MET cc_start: 0.6333 (mmm) cc_final: 0.5564 (tmm) outliers start: 5 outliers final: 0 residues processed: 232 average time/residue: 0.3847 time to fit residues: 144.3865 Evaluate side-chains 150 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 336 optimal weight: 0.0770 chunk 165 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 199 GLN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN B 924 ASN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 GLN C 635 GLN C 684 GLN C 886 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28819 Z= 0.202 Angle : 0.658 14.003 38944 Z= 0.345 Chirality : 0.044 0.234 4307 Planarity : 0.004 0.064 5056 Dihedral : 6.175 31.494 3789 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.14), residues: 3464 helix: -0.11 (0.13), residues: 1515 sheet: -1.68 (0.29), residues: 320 loop : -2.64 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 17 HIS 0.011 0.001 HIS G 34 PHE 0.028 0.001 PHE D 277 TYR 0.029 0.002 TYR D 123 ARG 0.006 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7595 (mpp) cc_final: 0.7124 (mmt) REVERT: B 130 MET cc_start: 0.7405 (mmm) cc_final: 0.6956 (mmm) REVERT: B 686 PHE cc_start: 0.9075 (m-10) cc_final: 0.8816 (m-80) REVERT: C 44 LEU cc_start: 0.8789 (mt) cc_final: 0.8442 (mt) REVERT: C 335 PHE cc_start: 0.8033 (t80) cc_final: 0.7702 (t80) REVERT: C 348 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8841 (mmmt) REVERT: C 542 LEU cc_start: 0.9124 (mt) cc_final: 0.8715 (mt) REVERT: C 737 MET cc_start: 0.8278 (mmm) cc_final: 0.7880 (mmm) REVERT: C 910 MET cc_start: 0.7248 (mmp) cc_final: 0.6408 (mmm) REVERT: E 291 ARG cc_start: 0.8045 (mpp80) cc_final: 0.7379 (tpm170) REVERT: F 17 MET cc_start: 0.7531 (ttm) cc_final: 0.7241 (ttm) REVERT: F 71 MET cc_start: 0.6543 (ptt) cc_final: 0.6217 (ppp) REVERT: F 89 LEU cc_start: 0.9175 (mm) cc_final: 0.8965 (mm) REVERT: F 93 LEU cc_start: 0.8740 (mt) cc_final: 0.8446 (mt) REVERT: G 17 MET cc_start: 0.8559 (mtp) cc_final: 0.8357 (mtt) REVERT: G 21 ASN cc_start: 0.8752 (m-40) cc_final: 0.8088 (m110) REVERT: G 51 ASP cc_start: 0.7930 (m-30) cc_final: 0.7729 (m-30) REVERT: A 100 MET cc_start: 0.6477 (mmm) cc_final: 0.5622 (tmm) REVERT: A 239 MET cc_start: 0.3749 (mmt) cc_final: 0.3236 (ppp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.4025 time to fit residues: 133.1370 Evaluate side-chains 135 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.0060 chunk 190 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 287 optimal weight: 0.0270 chunk 232 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.5614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 199 GLN B 388 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 ASN ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28819 Z= 0.145 Angle : 0.620 14.000 38944 Z= 0.320 Chirality : 0.043 0.224 4307 Planarity : 0.004 0.061 5056 Dihedral : 5.805 33.802 3789 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.80 (0.14), residues: 3464 helix: 0.17 (0.14), residues: 1514 sheet: -1.42 (0.29), residues: 323 loop : -2.55 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 285 HIS 0.006 0.001 HIS G 34 PHE 0.022 0.001 PHE D 277 TYR 0.030 0.001 TYR C 553 ARG 0.006 0.000 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.883 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: B 130 MET cc_start: 0.7172 (mmm) cc_final: 0.6793 (mmm) REVERT: B 161 LEU cc_start: 0.9303 (mt) cc_final: 0.9025 (mt) REVERT: B 422 LEU cc_start: 0.8603 (mt) cc_final: 0.8347 (mt) REVERT: B 604 MET cc_start: 0.1245 (ttt) cc_final: 0.0831 (tpp) REVERT: B 683 MET cc_start: 0.8735 (mmm) cc_final: 0.8496 (tpp) REVERT: B 686 PHE cc_start: 0.9103 (m-10) cc_final: 0.8854 (m-80) REVERT: B 753 MET cc_start: 0.8077 (mmm) cc_final: 0.7481 (mmm) REVERT: C 44 LEU cc_start: 0.8784 (mt) cc_final: 0.8517 (mt) REVERT: C 335 PHE cc_start: 0.7990 (t80) cc_final: 0.7699 (t80) REVERT: C 347 MET cc_start: 0.9279 (tmm) cc_final: 0.8609 (tmm) REVERT: C 348 LYS cc_start: 0.9144 (mmpt) cc_final: 0.8914 (mmmt) REVERT: C 542 LEU cc_start: 0.9173 (mt) cc_final: 0.8551 (mt) REVERT: C 737 MET cc_start: 0.8111 (mmm) cc_final: 0.7810 (mmm) REVERT: C 910 MET cc_start: 0.7428 (mmp) cc_final: 0.6619 (mmm) REVERT: D 93 CYS cc_start: 0.6651 (t) cc_final: 0.6316 (t) REVERT: E 265 MET cc_start: 0.8885 (pmm) cc_final: 0.8168 (pmm) REVERT: E 291 ARG cc_start: 0.7951 (mpp80) cc_final: 0.7358 (tpm170) REVERT: F 17 MET cc_start: 0.7479 (ttm) cc_final: 0.7163 (ttm) REVERT: F 71 MET cc_start: 0.6877 (ptt) cc_final: 0.6220 (ppp) REVERT: F 93 LEU cc_start: 0.8612 (mt) cc_final: 0.8370 (mt) REVERT: G 17 MET cc_start: 0.8721 (mtp) cc_final: 0.8488 (mtt) REVERT: G 21 ASN cc_start: 0.8656 (m110) cc_final: 0.8420 (m110) REVERT: G 51 ASP cc_start: 0.7897 (m-30) cc_final: 0.7621 (m-30) REVERT: G 78 ILE cc_start: 0.9080 (tt) cc_final: 0.8833 (mm) REVERT: A 100 MET cc_start: 0.6450 (mmm) cc_final: 0.5786 (tmm) REVERT: A 239 MET cc_start: 0.3499 (mmt) cc_final: 0.2888 (ppp) REVERT: A 244 VAL cc_start: 0.4560 (t) cc_final: 0.3915 (p) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3959 time to fit residues: 136.5976 Evaluate side-chains 138 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 279 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 370 ASN B 376 ASN B 431 GLN ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 249 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN ** C1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 215 HIS ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN D 414 GLN D 489 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28819 Z= 0.247 Angle : 0.686 13.332 38944 Z= 0.358 Chirality : 0.045 0.229 4307 Planarity : 0.004 0.061 5056 Dihedral : 5.996 32.692 3789 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.03 % Allowed : 1.97 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.84 (0.14), residues: 3464 helix: 0.12 (0.13), residues: 1535 sheet: -1.35 (0.30), residues: 323 loop : -2.62 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 17 HIS 0.007 0.001 HIS G 34 PHE 0.029 0.002 PHE D 277 TYR 0.024 0.002 TYR C 553 ARG 0.006 0.001 ARG D 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 3.355 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: B 130 MET cc_start: 0.7505 (mmm) cc_final: 0.7079 (mmm) REVERT: B 422 LEU cc_start: 0.8615 (mt) cc_final: 0.8397 (mt) REVERT: B 604 MET cc_start: 0.0321 (ttm) cc_final: -0.0239 (tpp) REVERT: B 683 MET cc_start: 0.8846 (mmm) cc_final: 0.8338 (tpp) REVERT: B 686 PHE cc_start: 0.9054 (m-10) cc_final: 0.8812 (m-80) REVERT: C 335 PHE cc_start: 0.8241 (t80) cc_final: 0.7899 (t80) REVERT: C 347 MET cc_start: 0.9349 (tmm) cc_final: 0.9084 (tmm) REVERT: C 348 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8823 (mmmt) REVERT: C 542 LEU cc_start: 0.9134 (mt) cc_final: 0.8734 (mt) REVERT: C 737 MET cc_start: 0.8363 (mmm) cc_final: 0.8003 (mmm) REVERT: C 753 MET cc_start: 0.8738 (mpp) cc_final: 0.8533 (mpp) REVERT: C 910 MET cc_start: 0.7237 (mmp) cc_final: 0.6275 (mmm) REVERT: D 393 PHE cc_start: 0.5693 (t80) cc_final: 0.5407 (t80) REVERT: E 265 MET cc_start: 0.8979 (pmm) cc_final: 0.8272 (pmm) REVERT: F 17 MET cc_start: 0.7566 (ttm) cc_final: 0.7154 (ttm) REVERT: F 71 MET cc_start: 0.6698 (ptt) cc_final: 0.6277 (ppp) REVERT: F 89 LEU cc_start: 0.9177 (mm) cc_final: 0.8946 (mm) REVERT: G 17 MET cc_start: 0.8760 (mtp) cc_final: 0.8491 (mtt) REVERT: G 21 ASN cc_start: 0.8843 (m110) cc_final: 0.8371 (m110) REVERT: G 51 ASP cc_start: 0.7998 (m-30) cc_final: 0.7786 (m-30) REVERT: G 78 ILE cc_start: 0.9113 (tt) cc_final: 0.8884 (mm) REVERT: A 100 MET cc_start: 0.6660 (mmm) cc_final: 0.5726 (tmm) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.3893 time to fit residues: 117.0507 Evaluate side-chains 124 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 8.9990 chunk 37 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 199 GLN B 370 ASN B 431 GLN C 46 ASN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28819 Z= 0.165 Angle : 0.635 13.825 38944 Z= 0.327 Chirality : 0.044 0.331 4307 Planarity : 0.004 0.063 5056 Dihedral : 5.738 34.035 3789 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.65 (0.14), residues: 3464 helix: 0.32 (0.14), residues: 1526 sheet: -1.27 (0.30), residues: 328 loop : -2.55 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 17 HIS 0.005 0.001 HIS D 244 PHE 0.029 0.001 PHE A 364 TYR 0.030 0.001 TYR C 553 ARG 0.005 0.000 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.317 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: B 130 MET cc_start: 0.7421 (mmm) cc_final: 0.6987 (mmm) REVERT: B 422 LEU cc_start: 0.8577 (mt) cc_final: 0.8355 (mt) REVERT: B 683 MET cc_start: 0.8862 (mmm) cc_final: 0.8442 (tpp) REVERT: B 753 MET cc_start: 0.8188 (mmm) cc_final: 0.7654 (mmm) REVERT: C 335 PHE cc_start: 0.8314 (t80) cc_final: 0.7877 (t80) REVERT: C 347 MET cc_start: 0.9332 (tmm) cc_final: 0.8914 (tmm) REVERT: C 348 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8912 (mmmt) REVERT: C 604 MET cc_start: 0.6810 (mmm) cc_final: 0.6579 (mmp) REVERT: C 737 MET cc_start: 0.8327 (mmm) cc_final: 0.8064 (mmm) REVERT: C 753 MET cc_start: 0.8764 (mpp) cc_final: 0.8562 (mpp) REVERT: C 910 MET cc_start: 0.7390 (mmp) cc_final: 0.6564 (mmm) REVERT: D 275 ASP cc_start: 0.6234 (p0) cc_final: 0.5984 (p0) REVERT: D 477 LYS cc_start: 0.7898 (pttt) cc_final: 0.7475 (tptt) REVERT: E 265 MET cc_start: 0.9071 (pmm) cc_final: 0.8194 (pmm) REVERT: F 17 MET cc_start: 0.7584 (ttm) cc_final: 0.7309 (ttm) REVERT: F 71 MET cc_start: 0.6839 (ptt) cc_final: 0.6435 (ppp) REVERT: F 93 LEU cc_start: 0.8645 (mt) cc_final: 0.8408 (mt) REVERT: G 17 MET cc_start: 0.8666 (mtp) cc_final: 0.8435 (mtt) REVERT: G 21 ASN cc_start: 0.8740 (m110) cc_final: 0.8188 (m-40) REVERT: G 51 ASP cc_start: 0.7954 (m-30) cc_final: 0.7653 (m-30) REVERT: G 65 PHE cc_start: 0.7079 (m-80) cc_final: 0.6865 (m-80) REVERT: G 71 MET cc_start: 0.8803 (ppp) cc_final: 0.8413 (ppp) REVERT: G 78 ILE cc_start: 0.9144 (tt) cc_final: 0.8927 (mm) REVERT: A 100 MET cc_start: 0.6436 (mmm) cc_final: 0.5519 (tpp) REVERT: A 239 MET cc_start: 0.2986 (tpp) cc_final: 0.2604 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3950 time to fit residues: 119.9258 Evaluate side-chains 126 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 65 optimal weight: 0.0370 chunk 64 optimal weight: 0.3980 chunk 213 optimal weight: 0.0470 chunk 228 optimal weight: 0.0970 chunk 165 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 263 optimal weight: 0.7980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN B 431 GLN C 234 ASN C 359 ASN C 370 ASN C 526 GLN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS C 958 GLN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28819 Z= 0.142 Angle : 0.618 14.578 38944 Z= 0.316 Chirality : 0.043 0.242 4307 Planarity : 0.004 0.060 5056 Dihedral : 5.361 33.022 3789 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.42 (0.14), residues: 3464 helix: 0.54 (0.14), residues: 1505 sheet: -1.24 (0.29), residues: 335 loop : -2.41 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 94 HIS 0.007 0.001 HIS D 244 PHE 0.031 0.001 PHE A 364 TYR 0.027 0.001 TYR C 553 ARG 0.006 0.000 ARG D 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 3.357 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: B 130 MET cc_start: 0.7108 (mmm) cc_final: 0.6730 (mmm) REVERT: B 422 LEU cc_start: 0.8521 (mt) cc_final: 0.8242 (mt) REVERT: B 683 MET cc_start: 0.8718 (mmm) cc_final: 0.8376 (tpp) REVERT: B 753 MET cc_start: 0.8195 (mmm) cc_final: 0.7774 (mmm) REVERT: B 1003 LEU cc_start: 0.9037 (tp) cc_final: 0.8629 (tt) REVERT: C 277 ILE cc_start: 0.9586 (mt) cc_final: 0.9263 (mt) REVERT: C 335 PHE cc_start: 0.8093 (t80) cc_final: 0.7840 (t80) REVERT: C 347 MET cc_start: 0.9260 (tmm) cc_final: 0.9046 (tmm) REVERT: C 348 LYS cc_start: 0.9277 (mmpt) cc_final: 0.8908 (mmmt) REVERT: C 390 MET cc_start: 0.7522 (tpp) cc_final: 0.7019 (tpp) REVERT: C 511 MET cc_start: 0.8998 (ppp) cc_final: 0.8766 (ppp) REVERT: C 604 MET cc_start: 0.6662 (mmm) cc_final: 0.6438 (mmp) REVERT: C 653 LEU cc_start: 0.8213 (tt) cc_final: 0.7417 (tt) REVERT: C 686 PHE cc_start: 0.8408 (m-10) cc_final: 0.8170 (m-80) REVERT: C 737 MET cc_start: 0.8202 (mmm) cc_final: 0.7957 (mmm) REVERT: C 910 MET cc_start: 0.7443 (mmp) cc_final: 0.6766 (mmm) REVERT: D 468 LEU cc_start: 0.6607 (tp) cc_final: 0.6307 (tp) REVERT: D 477 LYS cc_start: 0.7738 (pttt) cc_final: 0.7409 (tptt) REVERT: E 265 MET cc_start: 0.8896 (pmm) cc_final: 0.8258 (pmm) REVERT: F 17 MET cc_start: 0.7598 (ttm) cc_final: 0.7333 (ttm) REVERT: F 71 MET cc_start: 0.6988 (ptt) cc_final: 0.6638 (ppp) REVERT: G 21 ASN cc_start: 0.8756 (m110) cc_final: 0.8223 (m-40) REVERT: G 51 ASP cc_start: 0.7870 (m-30) cc_final: 0.7535 (m-30) REVERT: G 65 PHE cc_start: 0.6852 (m-80) cc_final: 0.5860 (m-80) REVERT: G 78 ILE cc_start: 0.9101 (tt) cc_final: 0.8894 (mm) REVERT: G 86 TYR cc_start: 0.8594 (t80) cc_final: 0.8322 (t80) REVERT: A 100 MET cc_start: 0.6356 (mmm) cc_final: 0.5696 (tmm) REVERT: A 294 ASN cc_start: 0.8753 (p0) cc_final: 0.8512 (m110) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3898 time to fit residues: 134.7713 Evaluate side-chains 143 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 293 optimal weight: 0.8980 chunk 312 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 0.0070 chunk 295 optimal weight: 6.9990 chunk 311 optimal weight: 7.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 199 GLN B 431 GLN C 359 ASN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 140 GLN ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28819 Z= 0.153 Angle : 0.618 14.484 38944 Z= 0.315 Chirality : 0.043 0.427 4307 Planarity : 0.004 0.061 5056 Dihedral : 5.287 33.209 3789 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.33 (0.15), residues: 3464 helix: 0.63 (0.14), residues: 1506 sheet: -1.19 (0.29), residues: 340 loop : -2.37 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 94 HIS 0.006 0.001 HIS C 680 PHE 0.028 0.001 PHE A 364 TYR 0.030 0.001 TYR C 553 ARG 0.005 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 3.058 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: B 130 MET cc_start: 0.7217 (mmm) cc_final: 0.6796 (mmm) REVERT: B 422 LEU cc_start: 0.8571 (mt) cc_final: 0.8290 (mt) REVERT: B 753 MET cc_start: 0.8334 (mmm) cc_final: 0.7841 (mmm) REVERT: B 1003 LEU cc_start: 0.9070 (tp) cc_final: 0.8677 (tt) REVERT: C 335 PHE cc_start: 0.8140 (t80) cc_final: 0.7846 (t80) REVERT: C 344 TYR cc_start: 0.7898 (t80) cc_final: 0.7493 (m-80) REVERT: C 347 MET cc_start: 0.9363 (tmm) cc_final: 0.9093 (tmm) REVERT: C 348 LYS cc_start: 0.9307 (mmpt) cc_final: 0.9047 (mmmt) REVERT: C 511 MET cc_start: 0.9012 (ppp) cc_final: 0.8803 (ppp) REVERT: C 604 MET cc_start: 0.6666 (mmm) cc_final: 0.6387 (mmp) REVERT: C 653 LEU cc_start: 0.8070 (tt) cc_final: 0.7666 (tt) REVERT: C 737 MET cc_start: 0.8394 (mmm) cc_final: 0.8133 (mmm) REVERT: C 753 MET cc_start: 0.8688 (mpp) cc_final: 0.8470 (mpp) REVERT: C 910 MET cc_start: 0.7490 (mmp) cc_final: 0.6837 (mmm) REVERT: D 275 ASP cc_start: 0.6379 (p0) cc_final: 0.6069 (p0) REVERT: D 477 LYS cc_start: 0.7681 (pttt) cc_final: 0.7453 (tptt) REVERT: E 265 MET cc_start: 0.8915 (pmm) cc_final: 0.8241 (pmm) REVERT: F 17 MET cc_start: 0.7585 (ttm) cc_final: 0.7312 (ttm) REVERT: F 71 MET cc_start: 0.6978 (ptt) cc_final: 0.6634 (ppp) REVERT: G 21 ASN cc_start: 0.8873 (m110) cc_final: 0.8323 (m110) REVERT: G 51 ASP cc_start: 0.8073 (m-30) cc_final: 0.7792 (m-30) REVERT: G 71 MET cc_start: 0.8731 (ppp) cc_final: 0.8337 (ppp) REVERT: G 78 ILE cc_start: 0.9152 (tt) cc_final: 0.8949 (mm) REVERT: G 86 TYR cc_start: 0.8610 (t80) cc_final: 0.8299 (t80) REVERT: A 100 MET cc_start: 0.6454 (mmm) cc_final: 0.5640 (tpp) REVERT: A 373 GLU cc_start: 0.8696 (tt0) cc_final: 0.8412 (tp30) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3807 time to fit residues: 117.9224 Evaluate side-chains 138 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.0870 chunk 330 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 156 optimal weight: 0.0970 chunk 229 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 319 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 199 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN C 359 ASN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 28819 Z= 0.147 Angle : 0.618 14.012 38944 Z= 0.313 Chirality : 0.043 0.260 4307 Planarity : 0.004 0.059 5056 Dihedral : 5.172 31.027 3789 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3464 helix: 0.68 (0.14), residues: 1505 sheet: -0.92 (0.30), residues: 325 loop : -2.38 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 285 HIS 0.006 0.001 HIS D 244 PHE 0.034 0.001 PHE D 177 TYR 0.028 0.001 TYR C 553 ARG 0.008 0.000 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 3.361 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: B 60 MET cc_start: 0.7922 (mpp) cc_final: 0.7472 (mmt) REVERT: B 130 MET cc_start: 0.7276 (mmm) cc_final: 0.6876 (mmm) REVERT: B 604 MET cc_start: -0.1735 (tpp) cc_final: -0.1942 (tpp) REVERT: B 753 MET cc_start: 0.8324 (mmm) cc_final: 0.7892 (mmm) REVERT: B 1003 LEU cc_start: 0.9070 (tp) cc_final: 0.8682 (tt) REVERT: C 335 PHE cc_start: 0.8086 (t80) cc_final: 0.7821 (t80) REVERT: C 344 TYR cc_start: 0.7703 (t80) cc_final: 0.7444 (m-80) REVERT: C 347 MET cc_start: 0.9335 (tmm) cc_final: 0.9036 (tmm) REVERT: C 348 LYS cc_start: 0.9271 (mmpt) cc_final: 0.9059 (mmmt) REVERT: C 511 MET cc_start: 0.8975 (ppp) cc_final: 0.8733 (ppp) REVERT: C 604 MET cc_start: 0.6485 (mmm) cc_final: 0.6228 (mmp) REVERT: C 653 LEU cc_start: 0.8034 (tt) cc_final: 0.7670 (tt) REVERT: C 686 PHE cc_start: 0.8195 (m-80) cc_final: 0.7637 (m-80) REVERT: C 737 MET cc_start: 0.8320 (mmm) cc_final: 0.8113 (mmm) REVERT: C 910 MET cc_start: 0.7455 (mmp) cc_final: 0.6794 (mmm) REVERT: E 265 MET cc_start: 0.8937 (pmm) cc_final: 0.8248 (pmm) REVERT: E 412 ASN cc_start: 0.8596 (p0) cc_final: 0.8013 (p0) REVERT: F 17 MET cc_start: 0.7482 (ttm) cc_final: 0.7277 (ttm) REVERT: G 21 ASN cc_start: 0.8876 (m110) cc_final: 0.8321 (m110) REVERT: G 51 ASP cc_start: 0.8052 (m-30) cc_final: 0.7794 (m-30) REVERT: G 86 TYR cc_start: 0.8562 (t80) cc_final: 0.8312 (t80) REVERT: A 100 MET cc_start: 0.6491 (mmm) cc_final: 0.5628 (tmm) REVERT: A 364 PHE cc_start: 0.7776 (m-80) cc_final: 0.7262 (m-80) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3864 time to fit residues: 120.4273 Evaluate side-chains 131 residues out of total 3094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.0870 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 254 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN B 234 ASN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS D 302 ASN ** D 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.080060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060559 restraints weight = 186159.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.061669 restraints weight = 120128.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.062527 restraints weight = 89099.478| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28819 Z= 0.139 Angle : 0.612 15.721 38944 Z= 0.310 Chirality : 0.043 0.253 4307 Planarity : 0.004 0.059 5056 Dihedral : 5.040 30.182 3789 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 1.89 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.21 (0.15), residues: 3464 helix: 0.72 (0.14), residues: 1499 sheet: -1.01 (0.30), residues: 339 loop : -2.30 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 94 HIS 0.006 0.001 HIS F 34 PHE 0.031 0.001 PHE A 364 TYR 0.031 0.001 TYR C 553 ARG 0.005 0.000 ARG B 352 =============================================================================== Job complete usr+sys time: 4751.84 seconds wall clock time: 88 minutes 3.50 seconds (5283.50 seconds total)