Starting phenix.real_space_refine on Wed Feb 14 02:08:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/02_2024/5mz6_3583.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5339 2.51 5 N 1457 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 20": "NH1" <-> "NH2" Residue "1 ARG 84": "NH1" <-> "NH2" Residue "1 ARG 153": "NH1" <-> "NH2" Residue "1 ARG 217": "NH1" <-> "NH2" Residue "1 ARG 252": "NH1" <-> "NH2" Residue "1 ARG 315": "NH1" <-> "NH2" Residue "1 ARG 492": "NH1" <-> "NH2" Residue "1 ARG 494": "NH1" <-> "NH2" Residue "1 ARG 504": "NH1" <-> "NH2" Residue "1 ARG 559": "NH1" <-> "NH2" Residue "1 ARG 631": "NH1" <-> "NH2" Residue "1 ARG 691": "NH1" <-> "NH2" Residue "1 ARG 697": "NH1" <-> "NH2" Residue "1 ARG 869": "NH1" <-> "NH2" Residue "1 ARG 930": "NH1" <-> "NH2" Residue "1 ARG 1044": "NH1" <-> "NH2" Residue "1 ARG 1116": "NH1" <-> "NH2" Residue "1 ARG 1120": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8401 Number of models: 1 Model: "" Number of chains: 2 Chain: "1" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7968 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 985} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 433 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 4.98, per 1000 atoms: 0.59 Number of scatterers: 8401 At special positions: 0 Unit cell: (88.66, 124.41, 74.36, 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 70 16.00 O 1535 8.00 N 1457 7.00 C 5339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 11031 " - pdb=" SG CYS 11066 " distance=2.02 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 63.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain '1' and resid 12 through 41 removed outlier: 3.938A pdb=" N LEU 1 16 " --> pdb=" O HIS 1 12 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU 1 18 " --> pdb=" O GLU 1 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS 1 21 " --> pdb=" O ASP 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 49 removed outlier: 4.045A pdb=" N ILE 1 46 " --> pdb=" O SER 1 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 58 No H-bonds generated for 'chain '1' and resid 56 through 58' Processing helix chain '1' and resid 59 through 72 removed outlier: 3.940A pdb=" N ARG 1 65 " --> pdb=" O SER 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 78 through 96 removed outlier: 4.198A pdb=" N TYR 1 82 " --> pdb=" O GLY 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 102 Processing helix chain '1' and resid 103 through 104 No H-bonds generated for 'chain '1' and resid 103 through 104' Processing helix chain '1' and resid 105 through 109 removed outlier: 3.531A pdb=" N ARG 1 108 " --> pdb=" O SER 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 125 removed outlier: 3.955A pdb=" N LEU 1 118 " --> pdb=" O ILE 1 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE 1 123 " --> pdb=" O CYS 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 143 removed outlier: 4.068A pdb=" N VAL 1 133 " --> pdb=" O CYS 1 129 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS 1 134 " --> pdb=" O ARG 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 144 through 149 Processing helix chain '1' and resid 150 through 158 removed outlier: 3.820A pdb=" N LEU 1 155 " --> pdb=" O ALA 1 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET 1 156 " --> pdb=" O LEU 1 152 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 171 removed outlier: 3.751A pdb=" N ILE 1 164 " --> pdb=" O GLU 1 160 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU 1 165 " --> pdb=" O THR 1 161 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 1 166 " --> pdb=" O GLU 1 162 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 1 170 " --> pdb=" O LYS 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 193 removed outlier: 3.630A pdb=" N ALA 1 183 " --> pdb=" O ASP 1 179 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 1 184 " --> pdb=" O MET 1 180 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU 1 191 " --> pdb=" O ALA 1 187 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS 1 192 " --> pdb=" O MET 1 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS 1 193 " --> pdb=" O ASN 1 189 " (cutoff:3.500A) Processing helix chain '1' and resid 198 through 214 removed outlier: 3.848A pdb=" N GLU 1 202 " --> pdb=" O VAL 1 198 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP 1 209 " --> pdb=" O MET 1 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS 1 212 " --> pdb=" O ARG 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 218 through 232 removed outlier: 3.701A pdb=" N TYR 1 227 " --> pdb=" O GLU 1 223 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 1 229 " --> pdb=" O ALA 1 225 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 237 removed outlier: 4.267A pdb=" N SER 1 236 " --> pdb=" O SER 1 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN 1 237 " --> pdb=" O THR 1 234 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 233 through 237' Processing helix chain '1' and resid 251 through 257 removed outlier: 4.165A pdb=" N HIS 1 255 " --> pdb=" O ASP 1 251 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 1 257 " --> pdb=" O VAL 1 253 " (cutoff:3.500A) Processing helix chain '1' and resid 258 through 271 removed outlier: 3.613A pdb=" N SER 1 263 " --> pdb=" O ALA 1 259 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP 1 264 " --> pdb=" O ALA 1 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 1 267 " --> pdb=" O SER 1 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 1 268 " --> pdb=" O ASP 1 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN 1 269 " --> pdb=" O SER 1 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 275 removed outlier: 4.123A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 275' Processing helix chain '1' and resid 304 through 321 removed outlier: 3.634A pdb=" N ILE 1 308 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 1 317 " --> pdb=" O GLU 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 329 through 346 removed outlier: 3.564A pdb=" N ALA 1 334 " --> pdb=" O ASP 1 330 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 1 336 " --> pdb=" O MET 1 332 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN 1 338 " --> pdb=" O ALA 1 334 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL 1 341 " --> pdb=" O LEU 1 337 " (cutoff:3.500A) Processing helix chain '1' and resid 347 through 365 removed outlier: 3.632A pdb=" N THR 1 354 " --> pdb=" O ARG 1 350 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR 1 357 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER 1 362 " --> pdb=" O LEU 1 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER 1 363 " --> pdb=" O ALA 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 386 removed outlier: 4.175A pdb=" N VAL 1 379 " --> pdb=" O LYS 1 375 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER 1 380 " --> pdb=" O LEU 1 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL 1 382 " --> pdb=" O ARG 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 451 through 456 removed outlier: 3.897A pdb=" N ILE 1 455 " --> pdb=" O ASN 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 475 removed outlier: 3.563A pdb=" N ALA 1 464 " --> pdb=" O SER 1 460 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET 1 467 " --> pdb=" O ALA 1 463 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 495 removed outlier: 3.545A pdb=" N ASP 1 486 " --> pdb=" O LYS 1 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 1 487 " --> pdb=" O HIS 1 483 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 1 489 " --> pdb=" O ASN 1 485 " (cutoff:3.500A) Processing helix chain '1' and resid 495 through 504 removed outlier: 3.829A pdb=" N GLN 1 499 " --> pdb=" O GLY 1 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 1 502 " --> pdb=" O SER 1 498 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS 1 503 " --> pdb=" O GLN 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 513 through 535 removed outlier: 3.519A pdb=" N LYS 1 530 " --> pdb=" O ARG 1 526 " (cutoff:3.500A) Processing helix chain '1' and resid 539 through 554 removed outlier: 3.960A pdb=" N MET 1 543 " --> pdb=" O ASP 1 539 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS 1 551 " --> pdb=" O ASN 1 547 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 1 553 " --> pdb=" O ALA 1 549 " (cutoff:3.500A) Processing helix chain '1' and resid 560 through 576 removed outlier: 3.826A pdb=" N ALA 1 566 " --> pdb=" O ASP 1 562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 1 567 " --> pdb=" O MET 1 563 " (cutoff:3.500A) Processing helix chain '1' and resid 629 through 645 removed outlier: 3.987A pdb=" N VAL 1 635 " --> pdb=" O ARG 1 631 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG 1 636 " --> pdb=" O PHE 1 632 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA 1 638 " --> pdb=" O LYS 1 634 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN 1 641 " --> pdb=" O LEU 1 637 " (cutoff:3.500A) Processing helix chain '1' and resid 651 through 666 removed outlier: 3.589A pdb=" N ARG 1 657 " --> pdb=" O GLU 1 653 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA 1 660 " --> pdb=" O CYS 1 656 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR 1 661 " --> pdb=" O ARG 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 669 through 679 removed outlier: 3.604A pdb=" N TYR 1 674 " --> pdb=" O TRP 1 670 " (cutoff:3.500A) Processing helix chain '1' and resid 681 through 693 removed outlier: 3.903A pdb=" N ALA 1 687 " --> pdb=" O GLY 1 683 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 1 688 " --> pdb=" O ALA 1 684 " (cutoff:3.500A) Processing helix chain '1' and resid 703 through 715 removed outlier: 3.630A pdb=" N ARG 1 707 " --> pdb=" O SER 1 703 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR 1 710 " --> pdb=" O ASP 1 706 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS 1 711 " --> pdb=" O ARG 1 707 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 1 712 " --> pdb=" O PHE 1 708 " (cutoff:3.500A) Processing helix chain '1' and resid 751 through 774 removed outlier: 3.645A pdb=" N LYS 1 760 " --> pdb=" O GLU 1 756 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 1 767 " --> pdb=" O PHE 1 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP 1 768 " --> pdb=" O LEU 1 764 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 1 771 " --> pdb=" O GLU 1 767 " (cutoff:3.500A) Processing helix chain '1' and resid 779 through 805 removed outlier: 3.597A pdb=" N TRP 1 784 " --> pdb=" O PRO 1 780 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG 1 787 " --> pdb=" O PHE 1 783 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE 1 789 " --> pdb=" O LYS 1 785 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 1 790 " --> pdb=" O ARG 1 786 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP 1 799 " --> pdb=" O MET 1 795 " (cutoff:3.500A) Processing helix chain '1' and resid 806 through 814 removed outlier: 3.626A pdb=" N ALA 1 810 " --> pdb=" O GLY 1 807 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET 1 814 " --> pdb=" O SER 1 811 " (cutoff:3.500A) Processing helix chain '1' and resid 823 through 834 removed outlier: 3.628A pdb=" N ALA 1 827 " --> pdb=" O ALA 1 823 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 1 828 " --> pdb=" O ALA 1 824 " (cutoff:3.500A) Processing helix chain '1' and resid 839 through 847 removed outlier: 3.869A pdb=" N GLU 1 845 " --> pdb=" O GLY 1 841 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET 1 846 " --> pdb=" O GLU 1 842 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 1 847 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) Processing helix chain '1' and resid 854 through 867 removed outlier: 3.605A pdb=" N LEU 1 863 " --> pdb=" O GLU 1 859 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS 1 866 " --> pdb=" O ILE 1 862 " (cutoff:3.500A) Processing helix chain '1' and resid 872 through 878 removed outlier: 3.572A pdb=" N LYS 1 876 " --> pdb=" O ASP 1 872 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 1 877 " --> pdb=" O GLU 1 873 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE 1 878 " --> pdb=" O LYS 1 874 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 872 through 878' Processing helix chain '1' and resid 879 through 891 removed outlier: 4.012A pdb=" N HIS 1 883 " --> pdb=" O LEU 1 879 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU 1 888 " --> pdb=" O ARG 1 884 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN 1 891 " --> pdb=" O VAL 1 887 " (cutoff:3.500A) Processing helix chain '1' and resid 933 through 947 Processing helix chain '1' and resid 956 through 959 removed outlier: 3.873A pdb=" N ASN 1 959 " --> pdb=" O ASP 1 956 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 956 through 959' Processing helix chain '1' and resid 965 through 969 removed outlier: 3.755A pdb=" N ASN 1 968 " --> pdb=" O ASP 1 965 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN 1 969 " --> pdb=" O PRO 1 966 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 965 through 969' Processing helix chain '1' and resid 971 through 984 removed outlier: 3.636A pdb=" N LYS 1 975 " --> pdb=" O GLY 1 971 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL 1 978 " --> pdb=" O GLN 1 974 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 1 979 " --> pdb=" O LYS 1 975 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR 1 980 " --> pdb=" O ARG 1 976 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 1 983 " --> pdb=" O GLU 1 979 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE 1 984 " --> pdb=" O TYR 1 980 " (cutoff:3.500A) Processing helix chain '1' and resid 995 through 1006 Processing helix chain '1' and resid 1022 through 1027 removed outlier: 3.683A pdb=" N LEU 11026 " --> pdb=" O PRO 11022 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 11027 " --> pdb=" O ARG 11023 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1022 through 1027' Processing helix chain '1' and resid 1057 through 1064 removed outlier: 3.683A pdb=" N TYR 11061 " --> pdb=" O ALA 11057 " (cutoff:3.500A) Processing helix chain '1' and resid 1079 through 1094 removed outlier: 3.517A pdb=" N ASP 11090 " --> pdb=" O ILE 11086 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP 11091 " --> pdb=" O ARG 11087 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE 11093 " --> pdb=" O ILE 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1107 through 1119 removed outlier: 3.595A pdb=" N HIS 11113 " --> pdb=" O SER 11109 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 11117 " --> pdb=" O HIS 11113 " (cutoff:3.500A) Processing helix chain '1' and resid 1125 through 1129 removed outlier: 3.753A pdb=" N VAL 11129 " --> pdb=" O GLY 11126 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.543A pdb=" N ALA B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 744 through 750 removed outlier: 7.004A pdb=" N ILE 1 732 " --> pdb=" O LEU 1 748 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN 1 931 " --> pdb=" O THR 1 903 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU 1 905 " --> pdb=" O GLN 1 931 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 953 through 955 removed outlier: 5.257A pdb=" N LEU 1 953 " --> pdb=" O VAL 11137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 987 through 990 removed outlier: 3.942A pdb=" N THR 1 989 " --> pdb=" O TYR 1 962 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU 1 964 " --> pdb=" O THR 1 989 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.68 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: 2719 1.34 - 1.46: 1952 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 8566 Sorted by residual: bond pdb=" C ARG B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.30e+00 bond pdb=" C LEU 1 879 " pdb=" N PRO 1 880 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.11e-02 8.12e+03 3.20e+00 bond pdb=" C LEU 11134 " pdb=" N PRO 11135 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.31e-02 5.83e+03 3.17e+00 bond pdb=" CB ASP 1 137 " pdb=" CG ASP 1 137 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.03e+00 bond pdb=" C ILE 1 114 " pdb=" N PRO 1 115 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 ... (remaining 8561 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 161 105.81 - 112.87: 4512 112.87 - 119.93: 2845 119.93 - 126.99: 3965 126.99 - 134.05: 102 Bond angle restraints: 11585 Sorted by residual: angle pdb=" N PRO B 148 " pdb=" CA PRO B 148 " pdb=" CB PRO B 148 " ideal model delta sigma weight residual 103.36 110.53 -7.17 8.80e-01 1.29e+00 6.64e+01 angle pdb=" N PRO B 168 " pdb=" CA PRO B 168 " pdb=" CB PRO B 168 " ideal model delta sigma weight residual 103.08 110.27 -7.19 9.70e-01 1.06e+00 5.50e+01 angle pdb=" N PRO B 169 " pdb=" CA PRO B 169 " pdb=" CB PRO B 169 " ideal model delta sigma weight residual 103.25 109.99 -6.74 1.05e+00 9.07e-01 4.12e+01 angle pdb=" N PRO B 172 " pdb=" CA PRO B 172 " pdb=" CB PRO B 172 " ideal model delta sigma weight residual 103.44 110.10 -6.66 1.12e+00 7.97e-01 3.53e+01 angle pdb=" CA ALA 11064 " pdb=" C ALA 11064 " pdb=" O ALA 11064 " ideal model delta sigma weight residual 119.43 113.44 5.99 1.21e+00 6.83e-01 2.45e+01 ... (remaining 11580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 4813 15.03 - 30.07: 263 30.07 - 45.10: 94 45.10 - 60.13: 12 60.13 - 75.16: 6 Dihedral angle restraints: 5188 sinusoidal: 1973 harmonic: 3215 Sorted by residual: dihedral pdb=" CA ILE 1 951 " pdb=" C ILE 1 951 " pdb=" N PRO 1 952 " pdb=" CA PRO 1 952 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA HIS 1 255 " pdb=" C HIS 1 255 " pdb=" N ILE 1 256 " pdb=" CA ILE 1 256 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PRO B 141 " pdb=" C PRO B 141 " pdb=" N TYR B 142 " pdb=" CA TYR B 142 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1098 0.065 - 0.131: 185 0.131 - 0.196: 21 0.196 - 0.261: 4 0.261 - 0.327: 2 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CB VAL 1 928 " pdb=" CA VAL 1 928 " pdb=" CG1 VAL 1 928 " pdb=" CG2 VAL 1 928 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE 1 271 " pdb=" CA ILE 1 271 " pdb=" CG1 ILE 1 271 " pdb=" CG2 ILE 1 271 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1307 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 1 951 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO 1 952 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO 1 952 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO 1 952 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 733 " -0.016 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR 1 733 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 733 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 733 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 733 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 733 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 1 733 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 1 733 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 484 " -0.018 2.00e-02 2.50e+03 1.72e-02 5.19e+00 pdb=" CG PHE 1 484 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE 1 484 " 0.001 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2343 2.79 - 3.32: 8018 3.32 - 3.85: 13964 3.85 - 4.37: 17024 4.37 - 4.90: 28108 Nonbonded interactions: 69457 Sorted by model distance: nonbonded pdb=" OH TYR 1 902 " pdb=" OE1 GLN 11107 " model vdw 2.269 2.440 nonbonded pdb=" O ILE 1 934 " pdb=" OG1 THR 1 937 " model vdw 2.279 2.440 nonbonded pdb=" CB ALA 1 772 " pdb=" OD2 ASP B 125 " model vdw 2.288 3.460 nonbonded pdb=" O ASP 1 539 " pdb=" OG1 THR 1 542 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR 1 124 " pdb=" O SER 1 345 " model vdw 2.331 2.440 ... (remaining 69452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.720 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8566 Z= 0.354 Angle : 1.046 14.517 11585 Z= 0.613 Chirality : 0.051 0.327 1310 Planarity : 0.007 0.071 1473 Dihedral : 11.570 75.163 3095 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.70 % Allowed : 5.10 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.18), residues: 1080 helix: -4.17 (0.10), residues: 573 sheet: -2.86 (0.74), residues: 45 loop : -2.57 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP 1 230 HIS 0.012 0.002 HIS 1 738 PHE 0.038 0.003 PHE 1 484 TYR 0.038 0.002 TYR 1 733 ARG 0.009 0.001 ARG 1 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 319 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8553 (tp30) cc_final: 0.8311 (tp30) REVERT: 1 65 ARG cc_start: 0.7941 (mtt180) cc_final: 0.6839 (mmt180) REVERT: 1 77 GLN cc_start: 0.8595 (tt0) cc_final: 0.8180 (tm-30) REVERT: 1 119 CYS cc_start: 0.8523 (t) cc_final: 0.8042 (m) REVERT: 1 153 ARG cc_start: 0.8443 (mtm110) cc_final: 0.8083 (mtp-110) REVERT: 1 177 SER cc_start: 0.7228 (m) cc_final: 0.6643 (p) REVERT: 1 188 MET cc_start: 0.8325 (ttp) cc_final: 0.7994 (mmt) REVERT: 1 202 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7661 (mm-30) REVERT: 1 203 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8465 (mptt) REVERT: 1 221 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.7798 (tmm160) REVERT: 1 261 LEU cc_start: 0.7733 (tt) cc_final: 0.7475 (tt) REVERT: 1 332 MET cc_start: 0.7759 (tpt) cc_final: 0.7521 (tpp) REVERT: 1 373 ASN cc_start: 0.8700 (t160) cc_final: 0.8442 (t0) REVERT: 1 466 TYR cc_start: 0.7356 (t80) cc_final: 0.6969 (t80) REVERT: 1 480 SER cc_start: 0.8858 (t) cc_final: 0.8619 (p) REVERT: 1 483 HIS cc_start: 0.7389 (t-90) cc_final: 0.6453 (t70) REVERT: 1 522 MET cc_start: 0.8485 (mtp) cc_final: 0.8036 (mtp) REVERT: 1 543 MET cc_start: 0.8333 (mmt) cc_final: 0.7924 (mpp) REVERT: 1 569 GLN cc_start: 0.8461 (tp40) cc_final: 0.7259 (tm-30) REVERT: 1 576 PHE cc_start: 0.7740 (m-10) cc_final: 0.7326 (m-10) REVERT: 1 582 TYR cc_start: 0.8066 (m-10) cc_final: 0.7567 (m-10) REVERT: 1 585 MET cc_start: 0.7534 (mmm) cc_final: 0.6627 (mmp) REVERT: 1 651 TYR cc_start: 0.8134 (m-10) cc_final: 0.7875 (m-10) REVERT: 1 653 GLU cc_start: 0.8857 (tp30) cc_final: 0.8501 (tp30) REVERT: 1 674 TYR cc_start: 0.8118 (t80) cc_final: 0.7439 (t80) REVERT: 1 693 GLU cc_start: 0.8172 (pt0) cc_final: 0.7767 (mt-10) REVERT: 1 768 ASP cc_start: 0.8712 (t0) cc_final: 0.8402 (t70) REVERT: 1 770 MET cc_start: 0.7456 (mmm) cc_final: 0.6810 (ppp) REVERT: 1 803 LYS cc_start: 0.8637 (mttt) cc_final: 0.8418 (mptt) REVERT: 1 876 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8332 (mmtm) REVERT: 1 906 VAL cc_start: 0.7535 (t) cc_final: 0.7235 (t) REVERT: 1 1036 LEU cc_start: 0.8256 (mp) cc_final: 0.7823 (tt) REVERT: 1 1038 MET cc_start: 0.7357 (mmt) cc_final: 0.6807 (mmm) REVERT: 1 1129 VAL cc_start: 0.9068 (t) cc_final: 0.8849 (p) REVERT: B 136 LEU cc_start: 0.8569 (tm) cc_final: 0.8194 (tp) outliers start: 6 outliers final: 0 residues processed: 319 average time/residue: 0.2378 time to fit residues: 99.4908 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 38 GLN 1 58 ASN 1 77 GLN 1 303 HIS 1 311 HIS 1 338 ASN 1 353 GLN 1 373 ASN 1 383 ASN 1 517 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 705 HIS ** 1 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 818 GLN 1 913 GLN 1 935 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8566 Z= 0.192 Angle : 0.621 8.102 11585 Z= 0.321 Chirality : 0.040 0.159 1310 Planarity : 0.005 0.058 1473 Dihedral : 5.481 27.174 1184 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.01 % Allowed : 13.90 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.32 (0.21), residues: 1080 helix: -2.11 (0.16), residues: 609 sheet: -2.00 (0.79), residues: 45 loop : -2.15 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 230 HIS 0.004 0.001 HIS 1 483 PHE 0.023 0.002 PHE 1 875 TYR 0.018 0.002 TYR 1 961 ARG 0.005 0.001 ARG 1 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 260 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8638 (tp30) cc_final: 0.8155 (tp30) REVERT: 1 20 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7690 (ttp80) REVERT: 1 24 SER cc_start: 0.8389 (t) cc_final: 0.8105 (p) REVERT: 1 56 ASP cc_start: 0.7628 (p0) cc_final: 0.7421 (p0) REVERT: 1 60 LEU cc_start: 0.9010 (tt) cc_final: 0.8630 (tp) REVERT: 1 65 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7182 (mmt180) REVERT: 1 77 GLN cc_start: 0.8548 (tt0) cc_final: 0.8125 (tm-30) REVERT: 1 119 CYS cc_start: 0.8764 (t) cc_final: 0.7868 (m) REVERT: 1 156 MET cc_start: 0.8258 (tpt) cc_final: 0.7861 (tpt) REVERT: 1 202 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7787 (mm-30) REVERT: 1 203 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8484 (mmtp) REVERT: 1 221 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7763 (tmm160) REVERT: 1 314 MET cc_start: 0.8868 (mmm) cc_final: 0.8565 (mmm) REVERT: 1 320 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8222 (tt) REVERT: 1 465 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8358 (mm-30) REVERT: 1 467 MET cc_start: 0.8633 (mmm) cc_final: 0.8311 (mmm) REVERT: 1 480 SER cc_start: 0.8847 (t) cc_final: 0.8599 (m) REVERT: 1 483 HIS cc_start: 0.7249 (t-90) cc_final: 0.6953 (t70) REVERT: 1 576 PHE cc_start: 0.7764 (m-10) cc_final: 0.7239 (m-10) REVERT: 1 585 MET cc_start: 0.7578 (mmm) cc_final: 0.7279 (mmp) REVERT: 1 633 GLU cc_start: 0.7983 (tp30) cc_final: 0.7644 (pp20) REVERT: 1 653 GLU cc_start: 0.8598 (tp30) cc_final: 0.8274 (tp30) REVERT: 1 693 GLU cc_start: 0.7903 (pt0) cc_final: 0.7694 (mt-10) REVERT: 1 746 MET cc_start: 0.8216 (ttm) cc_final: 0.7957 (ttp) REVERT: 1 751 TYR cc_start: 0.8066 (t80) cc_final: 0.7704 (t80) REVERT: 1 802 GLN cc_start: 0.8041 (tt0) cc_final: 0.7833 (tt0) REVERT: 1 803 LYS cc_start: 0.8728 (mttt) cc_final: 0.8467 (mmtt) REVERT: 1 846 MET cc_start: 0.8841 (mmm) cc_final: 0.8352 (mmp) REVERT: 1 866 CYS cc_start: 0.8972 (m) cc_final: 0.8387 (m) REVERT: 1 876 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8254 (mmtm) REVERT: 1 890 MET cc_start: 0.7461 (mmm) cc_final: 0.7226 (mmm) REVERT: 1 942 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7780 (tm-30) REVERT: 1 961 TYR cc_start: 0.7554 (t80) cc_final: 0.7150 (t80) REVERT: 1 977 MET cc_start: 0.8523 (tpt) cc_final: 0.8123 (tpt) REVERT: 1 1036 LEU cc_start: 0.8425 (mp) cc_final: 0.8187 (tt) REVERT: 1 1038 MET cc_start: 0.7862 (mmt) cc_final: 0.7429 (mmp) REVERT: 1 1065 LYS cc_start: 0.7379 (pttp) cc_final: 0.6949 (mtmt) REVERT: 1 1091 ASP cc_start: 0.8530 (t0) cc_final: 0.8112 (t0) REVERT: B 136 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8099 (tp) outliers start: 26 outliers final: 12 residues processed: 276 average time/residue: 0.2052 time to fit residues: 76.8001 Evaluate side-chains 240 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 710 THR Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 237 ASN 1 303 HIS 1 548 ASN ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN 1 750 HIS 1 883 HIS 1 910 HIS ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8566 Z= 0.309 Angle : 0.667 9.936 11585 Z= 0.341 Chirality : 0.043 0.189 1310 Planarity : 0.005 0.065 1473 Dihedral : 5.319 27.452 1184 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.87 % Allowed : 15.76 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1080 helix: -0.84 (0.19), residues: 601 sheet: -1.55 (0.85), residues: 45 loop : -1.62 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 1 154 HIS 0.005 0.002 HIS 1 738 PHE 0.024 0.002 PHE 1 922 TYR 0.020 0.002 TYR 1 138 ARG 0.003 0.001 ARG 1 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 GLU cc_start: 0.8550 (tp30) cc_final: 0.8228 (tp30) REVERT: 1 20 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7676 (ttp80) REVERT: 1 24 SER cc_start: 0.8159 (t) cc_final: 0.7906 (p) REVERT: 1 65 ARG cc_start: 0.8521 (mtt180) cc_final: 0.7478 (mmt180) REVERT: 1 77 GLN cc_start: 0.8816 (tt0) cc_final: 0.8056 (tm-30) REVERT: 1 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8516 (tp) REVERT: 1 156 MET cc_start: 0.8231 (tpt) cc_final: 0.7914 (tpt) REVERT: 1 188 MET cc_start: 0.8635 (tpt) cc_final: 0.8358 (tpt) REVERT: 1 202 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7796 (mm-30) REVERT: 1 221 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.7748 (tmm160) REVERT: 1 264 ASP cc_start: 0.7222 (t0) cc_final: 0.6584 (t0) REVERT: 1 467 MET cc_start: 0.8867 (mmm) cc_final: 0.8481 (mmm) REVERT: 1 480 SER cc_start: 0.8965 (t) cc_final: 0.8647 (m) REVERT: 1 482 LYS cc_start: 0.8518 (tmtp) cc_final: 0.7963 (tptp) REVERT: 1 483 HIS cc_start: 0.7097 (t-90) cc_final: 0.6796 (t70) REVERT: 1 570 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8478 (mp) REVERT: 1 576 PHE cc_start: 0.7474 (m-80) cc_final: 0.7161 (m-10) REVERT: 1 585 MET cc_start: 0.7658 (mmm) cc_final: 0.7158 (mmp) REVERT: 1 633 GLU cc_start: 0.8265 (tp30) cc_final: 0.7837 (pp20) REVERT: 1 653 GLU cc_start: 0.8865 (tp30) cc_final: 0.8469 (tp30) REVERT: 1 702 MET cc_start: 0.7297 (mmp) cc_final: 0.6914 (mmp) REVERT: 1 707 ARG cc_start: 0.8400 (tmt170) cc_final: 0.8132 (tpt90) REVERT: 1 751 TYR cc_start: 0.8231 (t80) cc_final: 0.7907 (t80) REVERT: 1 802 GLN cc_start: 0.8046 (tt0) cc_final: 0.7834 (tt0) REVERT: 1 803 LYS cc_start: 0.8590 (mttt) cc_final: 0.8344 (mmtt) REVERT: 1 846 MET cc_start: 0.8407 (mmm) cc_final: 0.7237 (mmm) REVERT: 1 876 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8284 (mmtm) REVERT: 1 892 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7519 (mt0) REVERT: 1 906 VAL cc_start: 0.7558 (t) cc_final: 0.7347 (t) REVERT: 1 935 HIS cc_start: 0.7729 (m-70) cc_final: 0.7506 (m170) REVERT: 1 942 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7853 (tm-30) REVERT: 1 961 TYR cc_start: 0.7508 (t80) cc_final: 0.7214 (t80) REVERT: 1 964 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6193 (mt) REVERT: 1 977 MET cc_start: 0.8557 (tpt) cc_final: 0.8171 (tpt) REVERT: 1 1021 MET cc_start: 0.8422 (ppp) cc_final: 0.7183 (ppp) REVERT: 1 1036 LEU cc_start: 0.8490 (mp) cc_final: 0.8156 (tt) REVERT: 1 1091 ASP cc_start: 0.8678 (t0) cc_final: 0.8100 (t0) REVERT: 1 1105 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6333 (mt) REVERT: 1 1106 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7089 (mmp80) outliers start: 42 outliers final: 26 residues processed: 249 average time/residue: 0.2128 time to fit residues: 71.9993 Evaluate side-chains 236 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 355 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 458 LEU Chi-restraints excluded: chain 1 residue 469 SER Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 710 THR Chi-restraints excluded: chain 1 residue 713 GLN Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1075 THR Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 HIS ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8566 Z= 0.238 Angle : 0.617 8.676 11585 Z= 0.309 Chirality : 0.041 0.133 1310 Planarity : 0.004 0.065 1473 Dihedral : 5.016 25.580 1184 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.63 % Allowed : 16.80 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1080 helix: -0.11 (0.21), residues: 594 sheet: -0.63 (0.91), residues: 40 loop : -1.50 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 1 154 HIS 0.005 0.001 HIS 1 738 PHE 0.021 0.002 PHE 1 123 TYR 0.017 0.002 TYR 1 138 ARG 0.004 0.000 ARG 1 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7613 (ttp80) REVERT: 1 24 SER cc_start: 0.8086 (t) cc_final: 0.7837 (p) REVERT: 1 65 ARG cc_start: 0.8612 (mtt180) cc_final: 0.7653 (mmt180) REVERT: 1 77 GLN cc_start: 0.8838 (tt0) cc_final: 0.8076 (tm-30) REVERT: 1 128 LEU cc_start: 0.8918 (tp) cc_final: 0.8412 (tp) REVERT: 1 156 MET cc_start: 0.8253 (tpt) cc_final: 0.7742 (tpt) REVERT: 1 188 MET cc_start: 0.8579 (tpt) cc_final: 0.8225 (tpt) REVERT: 1 202 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7855 (mm-30) REVERT: 1 221 ARG cc_start: 0.8507 (tpp-160) cc_final: 0.7748 (tmm160) REVERT: 1 264 ASP cc_start: 0.7219 (t0) cc_final: 0.6906 (t0) REVERT: 1 466 TYR cc_start: 0.7863 (t80) cc_final: 0.7225 (t80) REVERT: 1 467 MET cc_start: 0.8892 (mmm) cc_final: 0.8410 (mmm) REVERT: 1 469 SER cc_start: 0.9166 (m) cc_final: 0.8959 (t) REVERT: 1 480 SER cc_start: 0.8961 (t) cc_final: 0.8670 (m) REVERT: 1 482 LYS cc_start: 0.8535 (tmtp) cc_final: 0.7984 (tptp) REVERT: 1 483 HIS cc_start: 0.7203 (t-90) cc_final: 0.6985 (t70) REVERT: 1 570 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8419 (mp) REVERT: 1 576 PHE cc_start: 0.7558 (m-80) cc_final: 0.7146 (m-10) REVERT: 1 585 MET cc_start: 0.8013 (mmm) cc_final: 0.7445 (mmp) REVERT: 1 633 GLU cc_start: 0.8228 (tp30) cc_final: 0.7827 (pp20) REVERT: 1 653 GLU cc_start: 0.8797 (tp30) cc_final: 0.8580 (tp30) REVERT: 1 702 MET cc_start: 0.7399 (mmp) cc_final: 0.6880 (mmp) REVERT: 1 726 MET cc_start: 0.8317 (mtp) cc_final: 0.8062 (mtm) REVERT: 1 751 TYR cc_start: 0.7998 (t80) cc_final: 0.7561 (t80) REVERT: 1 768 ASP cc_start: 0.8554 (t0) cc_final: 0.8349 (t0) REVERT: 1 803 LYS cc_start: 0.8656 (mttt) cc_final: 0.8382 (mmtt) REVERT: 1 846 MET cc_start: 0.8442 (mmm) cc_final: 0.7616 (mmm) REVERT: 1 892 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7560 (mt0) REVERT: 1 935 HIS cc_start: 0.7655 (m-70) cc_final: 0.7080 (m170) REVERT: 1 942 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7850 (tm-30) REVERT: 1 961 TYR cc_start: 0.7497 (t80) cc_final: 0.7134 (t80) REVERT: 1 977 MET cc_start: 0.8551 (tpt) cc_final: 0.8176 (tpt) REVERT: 1 1021 MET cc_start: 0.8604 (ppp) cc_final: 0.8283 (ppp) REVERT: 1 1036 LEU cc_start: 0.8545 (mp) cc_final: 0.8239 (tt) REVERT: 1 1091 ASP cc_start: 0.8714 (t0) cc_final: 0.8140 (t0) REVERT: 1 1105 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6333 (mt) REVERT: 1 1106 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7192 (mmp80) outliers start: 40 outliers final: 27 residues processed: 244 average time/residue: 0.2044 time to fit residues: 68.4059 Evaluate side-chains 238 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 184 THR Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 320 LEU Chi-restraints excluded: chain 1 residue 355 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 921 ILE Chi-restraints excluded: chain 1 residue 955 ILE Chi-restraints excluded: chain 1 residue 973 THR Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1075 THR Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 HIS 1 573 GLN ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 974 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8566 Z= 0.314 Angle : 0.667 8.323 11585 Z= 0.337 Chirality : 0.043 0.162 1310 Planarity : 0.005 0.068 1473 Dihedral : 5.163 26.705 1184 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.45 % Allowed : 17.84 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1080 helix: 0.05 (0.21), residues: 602 sheet: -1.33 (0.83), residues: 45 loop : -1.43 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 1 154 HIS 0.006 0.001 HIS 1 738 PHE 0.027 0.002 PHE 1 123 TYR 0.018 0.002 TYR 1 582 ARG 0.004 0.001 ARG 1 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 215 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7545 (ttp80) REVERT: 1 65 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7662 (mmt180) REVERT: 1 77 GLN cc_start: 0.9090 (tt0) cc_final: 0.8335 (tm-30) REVERT: 1 128 LEU cc_start: 0.9013 (tp) cc_final: 0.8489 (tp) REVERT: 1 156 MET cc_start: 0.8268 (tpt) cc_final: 0.7812 (tpt) REVERT: 1 188 MET cc_start: 0.8619 (tpt) cc_final: 0.7606 (tpt) REVERT: 1 202 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7730 (mm-30) REVERT: 1 221 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.7576 (tmm160) REVERT: 1 264 ASP cc_start: 0.7639 (t0) cc_final: 0.7355 (t0) REVERT: 1 465 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8235 (mm-30) REVERT: 1 466 TYR cc_start: 0.7864 (t80) cc_final: 0.7306 (t80) REVERT: 1 467 MET cc_start: 0.8926 (mmm) cc_final: 0.7979 (mmm) REVERT: 1 469 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8977 (t) REVERT: 1 480 SER cc_start: 0.9009 (t) cc_final: 0.8716 (m) REVERT: 1 483 HIS cc_start: 0.7181 (t-90) cc_final: 0.6817 (t-90) REVERT: 1 570 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (mp) REVERT: 1 576 PHE cc_start: 0.7617 (m-80) cc_final: 0.7176 (m-10) REVERT: 1 585 MET cc_start: 0.8051 (mmm) cc_final: 0.7464 (mmp) REVERT: 1 633 GLU cc_start: 0.8307 (tp30) cc_final: 0.7868 (pp20) REVERT: 1 768 ASP cc_start: 0.8547 (t0) cc_final: 0.8309 (t0) REVERT: 1 803 LYS cc_start: 0.8656 (mttt) cc_final: 0.8331 (mmtt) REVERT: 1 846 MET cc_start: 0.8342 (mmm) cc_final: 0.7489 (mmm) REVERT: 1 892 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7645 (mt0) REVERT: 1 935 HIS cc_start: 0.7677 (m-70) cc_final: 0.7062 (m170) REVERT: 1 961 TYR cc_start: 0.7561 (t80) cc_final: 0.7255 (t80) REVERT: 1 964 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6466 (mt) REVERT: 1 977 MET cc_start: 0.8435 (tpt) cc_final: 0.8156 (tpt) REVERT: 1 1021 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7315 (ppp) REVERT: 1 1036 LEU cc_start: 0.8648 (mp) cc_final: 0.8268 (tt) REVERT: 1 1091 ASP cc_start: 0.8694 (t0) cc_final: 0.8203 (t0) REVERT: 1 1105 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6010 (mt) REVERT: 1 1106 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7262 (mmp80) outliers start: 47 outliers final: 27 residues processed: 240 average time/residue: 0.1983 time to fit residues: 65.9174 Evaluate side-chains 235 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 184 THR Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 355 THR Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 458 LEU Chi-restraints excluded: chain 1 residue 469 SER Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 705 HIS Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1075 THR Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 HIS 1 644 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 974 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8566 Z= 0.177 Angle : 0.604 9.626 11585 Z= 0.298 Chirality : 0.040 0.134 1310 Planarity : 0.004 0.065 1473 Dihedral : 4.825 27.664 1184 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.06 % Allowed : 19.58 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1080 helix: 0.45 (0.21), residues: 602 sheet: -0.27 (0.89), residues: 40 loop : -1.52 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 PHE 0.022 0.002 PHE 1 123 TYR 0.020 0.001 TYR 1 138 ARG 0.004 0.000 ARG 1 652 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7636 (ttp-110) REVERT: 1 65 ARG cc_start: 0.8645 (mtt180) cc_final: 0.7682 (mmt180) REVERT: 1 77 GLN cc_start: 0.9037 (tt0) cc_final: 0.8334 (tm-30) REVERT: 1 128 LEU cc_start: 0.8848 (tp) cc_final: 0.8521 (tp) REVERT: 1 144 ASP cc_start: 0.8183 (t0) cc_final: 0.7957 (t0) REVERT: 1 156 MET cc_start: 0.8256 (tpt) cc_final: 0.8025 (tpt) REVERT: 1 188 MET cc_start: 0.8449 (tpt) cc_final: 0.8133 (tpt) REVERT: 1 202 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7778 (mm-30) REVERT: 1 221 ARG cc_start: 0.8433 (tpp-160) cc_final: 0.7556 (tmm160) REVERT: 1 264 ASP cc_start: 0.7529 (t0) cc_final: 0.7270 (t0) REVERT: 1 465 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8134 (mm-30) REVERT: 1 466 TYR cc_start: 0.7824 (t80) cc_final: 0.7162 (t80) REVERT: 1 467 MET cc_start: 0.8929 (mmm) cc_final: 0.8392 (mmm) REVERT: 1 480 SER cc_start: 0.8994 (t) cc_final: 0.8712 (m) REVERT: 1 483 HIS cc_start: 0.7169 (t-90) cc_final: 0.6808 (t-90) REVERT: 1 569 GLN cc_start: 0.8406 (tp40) cc_final: 0.7747 (tm-30) REVERT: 1 570 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8505 (mp) REVERT: 1 576 PHE cc_start: 0.7549 (m-80) cc_final: 0.7202 (m-10) REVERT: 1 633 GLU cc_start: 0.8278 (tp30) cc_final: 0.7826 (pp20) REVERT: 1 795 MET cc_start: 0.8504 (tmm) cc_final: 0.8119 (tmm) REVERT: 1 803 LYS cc_start: 0.8690 (mttt) cc_final: 0.8418 (mmtt) REVERT: 1 846 MET cc_start: 0.8248 (mmm) cc_final: 0.7961 (mmp) REVERT: 1 922 PHE cc_start: 0.8825 (m-80) cc_final: 0.8618 (m-80) REVERT: 1 935 HIS cc_start: 0.7528 (m-70) cc_final: 0.7216 (m170) REVERT: 1 961 TYR cc_start: 0.7586 (t80) cc_final: 0.7312 (t80) REVERT: 1 964 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6546 (mt) REVERT: 1 977 MET cc_start: 0.8437 (tpt) cc_final: 0.8190 (tpt) REVERT: 1 1021 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7277 (ppp) REVERT: 1 1038 MET cc_start: 0.8122 (mmt) cc_final: 0.7547 (mmt) REVERT: 1 1091 ASP cc_start: 0.8773 (t0) cc_final: 0.8377 (t0) REVERT: 1 1105 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6001 (mt) REVERT: 1 1106 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7233 (mmp80) outliers start: 35 outliers final: 23 residues processed: 249 average time/residue: 0.1991 time to fit residues: 68.3060 Evaluate side-chains 232 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 271 ILE Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 281 ASN Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1075 THR Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN ** 1 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 689 GLN ** 1 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8566 Z= 0.221 Angle : 0.622 8.443 11585 Z= 0.310 Chirality : 0.041 0.161 1310 Planarity : 0.004 0.066 1473 Dihedral : 4.816 27.204 1184 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.10 % Allowed : 20.97 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1080 helix: 0.56 (0.21), residues: 608 sheet: -0.90 (0.84), residues: 45 loop : -1.49 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 PHE 0.019 0.002 PHE 1 123 TYR 0.019 0.001 TYR 1 138 ARG 0.006 0.000 ARG 1 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 207 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7683 (ttp80) REVERT: 1 65 ARG cc_start: 0.8644 (mtt180) cc_final: 0.7684 (mmt180) REVERT: 1 77 GLN cc_start: 0.9059 (tt0) cc_final: 0.8349 (tm-30) REVERT: 1 128 LEU cc_start: 0.8956 (tp) cc_final: 0.8491 (tp) REVERT: 1 188 MET cc_start: 0.8410 (tpt) cc_final: 0.7505 (tpt) REVERT: 1 202 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8025 (mm-30) REVERT: 1 221 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.7546 (tmm160) REVERT: 1 465 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8269 (mm-30) REVERT: 1 466 TYR cc_start: 0.7811 (t80) cc_final: 0.7239 (t80) REVERT: 1 467 MET cc_start: 0.8853 (mmm) cc_final: 0.8277 (mmm) REVERT: 1 480 SER cc_start: 0.9008 (t) cc_final: 0.8706 (m) REVERT: 1 483 HIS cc_start: 0.7123 (t-90) cc_final: 0.6731 (t-90) REVERT: 1 555 TYR cc_start: 0.7914 (m-80) cc_final: 0.7458 (m-80) REVERT: 1 562 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7642 (p0) REVERT: 1 569 GLN cc_start: 0.8398 (tp40) cc_final: 0.7739 (tm-30) REVERT: 1 570 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8491 (mp) REVERT: 1 576 PHE cc_start: 0.7631 (m-80) cc_final: 0.7319 (m-10) REVERT: 1 585 MET cc_start: 0.7949 (mmp) cc_final: 0.7555 (mmp) REVERT: 1 633 GLU cc_start: 0.8336 (tp30) cc_final: 0.7857 (pp20) REVERT: 1 795 MET cc_start: 0.8629 (tmm) cc_final: 0.8254 (tmm) REVERT: 1 803 LYS cc_start: 0.8714 (mttt) cc_final: 0.8400 (mmtt) REVERT: 1 839 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8041 (mp) REVERT: 1 846 MET cc_start: 0.8321 (mmm) cc_final: 0.7980 (mmp) REVERT: 1 961 TYR cc_start: 0.7596 (t80) cc_final: 0.7308 (t80) REVERT: 1 964 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6347 (mt) REVERT: 1 977 MET cc_start: 0.8458 (tpt) cc_final: 0.8158 (tpt) REVERT: 1 1021 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7299 (ppp) REVERT: 1 1038 MET cc_start: 0.8223 (mmt) cc_final: 0.7650 (mmt) REVERT: 1 1091 ASP cc_start: 0.8750 (t0) cc_final: 0.8404 (t0) REVERT: 1 1105 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6061 (mt) REVERT: 1 1106 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7284 (mmp80) outliers start: 44 outliers final: 33 residues processed: 229 average time/residue: 0.1997 time to fit residues: 63.7566 Evaluate side-chains 236 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 271 ILE Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 281 ASN Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 562 ASP Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 689 GLN Chi-restraints excluded: chain 1 residue 705 HIS Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 839 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1070 VAL Chi-restraints excluded: chain 1 residue 1075 THR Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 GLN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8566 Z= 0.191 Angle : 0.616 9.381 11585 Z= 0.304 Chirality : 0.040 0.155 1310 Planarity : 0.004 0.065 1473 Dihedral : 4.712 27.225 1184 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.75 % Allowed : 21.09 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1080 helix: 0.69 (0.21), residues: 611 sheet: -0.05 (0.89), residues: 40 loop : -1.55 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 1 154 HIS 0.005 0.001 HIS 1 738 PHE 0.020 0.002 PHE 11084 TYR 0.020 0.001 TYR 1 138 ARG 0.004 0.000 ARG 1 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7778 (ttp80) REVERT: 1 65 ARG cc_start: 0.8634 (mtt180) cc_final: 0.7673 (mmt180) REVERT: 1 77 GLN cc_start: 0.9051 (tt0) cc_final: 0.8356 (tm-30) REVERT: 1 128 LEU cc_start: 0.8830 (tp) cc_final: 0.8412 (tp) REVERT: 1 202 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8014 (mm-30) REVERT: 1 221 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7687 (tmm160) REVERT: 1 388 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.6188 (p0) REVERT: 1 465 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8221 (mm-30) REVERT: 1 466 TYR cc_start: 0.7847 (t80) cc_final: 0.7309 (t80) REVERT: 1 467 MET cc_start: 0.8854 (mmm) cc_final: 0.8281 (mmm) REVERT: 1 480 SER cc_start: 0.9004 (t) cc_final: 0.8545 (p) REVERT: 1 483 HIS cc_start: 0.7126 (t-90) cc_final: 0.6782 (t-90) REVERT: 1 555 TYR cc_start: 0.7830 (m-80) cc_final: 0.7314 (m-80) REVERT: 1 562 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7610 (p0) REVERT: 1 569 GLN cc_start: 0.8392 (tp40) cc_final: 0.7717 (tm-30) REVERT: 1 570 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8473 (mp) REVERT: 1 585 MET cc_start: 0.7960 (mmp) cc_final: 0.7145 (mmp) REVERT: 1 633 GLU cc_start: 0.8326 (tp30) cc_final: 0.7831 (pp20) REVERT: 1 678 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: 1 758 MET cc_start: 0.8493 (mmm) cc_final: 0.8264 (tpp) REVERT: 1 795 MET cc_start: 0.8627 (tmm) cc_final: 0.8273 (tmm) REVERT: 1 839 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8017 (mp) REVERT: 1 846 MET cc_start: 0.8275 (mmm) cc_final: 0.7923 (mmp) REVERT: 1 958 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7656 (tp40) REVERT: 1 961 TYR cc_start: 0.7373 (t80) cc_final: 0.7165 (t80) REVERT: 1 964 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6409 (mt) REVERT: 1 977 MET cc_start: 0.8496 (tpt) cc_final: 0.8226 (tpt) REVERT: 1 1021 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7198 (ppp) REVERT: 1 1038 MET cc_start: 0.8317 (mmt) cc_final: 0.7668 (mmt) REVERT: 1 1091 ASP cc_start: 0.8708 (t0) cc_final: 0.8409 (t0) REVERT: 1 1105 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6081 (mt) REVERT: 1 1106 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7257 (mmp80) outliers start: 41 outliers final: 27 residues processed: 230 average time/residue: 0.1868 time to fit residues: 60.6941 Evaluate side-chains 233 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 281 ASN Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 523 CYS Chi-restraints excluded: chain 1 residue 562 ASP Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 573 GLN Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 678 GLU Chi-restraints excluded: chain 1 residue 705 HIS Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 839 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 868 MET Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8566 Z= 0.168 Angle : 0.619 10.407 11585 Z= 0.303 Chirality : 0.039 0.165 1310 Planarity : 0.004 0.062 1473 Dihedral : 4.560 26.987 1184 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.94 % Allowed : 22.25 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1080 helix: 0.82 (0.21), residues: 612 sheet: -0.64 (0.85), residues: 45 loop : -1.35 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 PHE 0.023 0.001 PHE 1 546 TYR 0.020 0.001 TYR 1 138 ARG 0.004 0.000 ARG 1 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7765 (ttp80) REVERT: 1 65 ARG cc_start: 0.8630 (mtt180) cc_final: 0.7649 (mmt180) REVERT: 1 75 TYR cc_start: 0.7304 (m-80) cc_final: 0.6984 (m-80) REVERT: 1 77 GLN cc_start: 0.9040 (tt0) cc_final: 0.8135 (tm-30) REVERT: 1 128 LEU cc_start: 0.8861 (tp) cc_final: 0.8431 (tp) REVERT: 1 153 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8208 (mtm110) REVERT: 1 156 MET cc_start: 0.8424 (mmm) cc_final: 0.8199 (mmm) REVERT: 1 202 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8005 (mm-30) REVERT: 1 221 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.7698 (tmm160) REVERT: 1 388 ASN cc_start: 0.6378 (OUTLIER) cc_final: 0.6147 (p0) REVERT: 1 465 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8200 (mm-30) REVERT: 1 466 TYR cc_start: 0.7833 (t80) cc_final: 0.7312 (t80) REVERT: 1 467 MET cc_start: 0.8846 (mmm) cc_final: 0.8268 (mmm) REVERT: 1 480 SER cc_start: 0.9007 (t) cc_final: 0.8533 (p) REVERT: 1 483 HIS cc_start: 0.7029 (t-90) cc_final: 0.6822 (t-90) REVERT: 1 547 ASN cc_start: 0.8781 (m-40) cc_final: 0.8381 (m-40) REVERT: 1 555 TYR cc_start: 0.7698 (m-80) cc_final: 0.7246 (m-80) REVERT: 1 562 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7704 (p0) REVERT: 1 569 GLN cc_start: 0.8379 (tp40) cc_final: 0.7631 (tm-30) REVERT: 1 570 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (mp) REVERT: 1 585 MET cc_start: 0.7974 (mmp) cc_final: 0.7537 (mmp) REVERT: 1 633 GLU cc_start: 0.8230 (tp30) cc_final: 0.7756 (pp20) REVERT: 1 678 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: 1 758 MET cc_start: 0.8472 (mmm) cc_final: 0.8268 (tpp) REVERT: 1 761 PHE cc_start: 0.7666 (t80) cc_final: 0.7439 (t80) REVERT: 1 839 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7988 (mp) REVERT: 1 846 MET cc_start: 0.8057 (mmm) cc_final: 0.7789 (mmp) REVERT: 1 958 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7647 (tp40) REVERT: 1 961 TYR cc_start: 0.7055 (t80) cc_final: 0.6835 (t80) REVERT: 1 964 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6381 (mt) REVERT: 1 977 MET cc_start: 0.8499 (tpt) cc_final: 0.8181 (tpt) REVERT: 1 1021 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7506 (ppp) REVERT: 1 1038 MET cc_start: 0.8363 (mmt) cc_final: 0.7632 (mmt) REVERT: 1 1091 ASP cc_start: 0.8578 (t0) cc_final: 0.8369 (t0) REVERT: 1 1105 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6376 (mt) REVERT: 1 1106 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7234 (mmp80) outliers start: 34 outliers final: 24 residues processed: 230 average time/residue: 0.1912 time to fit residues: 61.9291 Evaluate side-chains 236 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 281 ASN Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 388 ASN Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 562 ASP Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 678 GLU Chi-restraints excluded: chain 1 residue 705 HIS Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 839 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 52 ASN 1 77 GLN 1 303 HIS 1 517 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 974 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8566 Z= 0.197 Angle : 0.624 10.922 11585 Z= 0.308 Chirality : 0.040 0.176 1310 Planarity : 0.004 0.059 1473 Dihedral : 4.553 26.737 1184 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.17 % Allowed : 22.48 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1080 helix: 0.88 (0.21), residues: 614 sheet: 0.23 (0.88), residues: 40 loop : -1.37 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 PHE 0.014 0.002 PHE 11010 TYR 0.019 0.001 TYR 1 138 ARG 0.004 0.000 ARG 1 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 20 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7763 (ttp80) REVERT: 1 65 ARG cc_start: 0.8631 (mtt180) cc_final: 0.7649 (mmt180) REVERT: 1 77 GLN cc_start: 0.9146 (tt0) cc_final: 0.8082 (tm-30) REVERT: 1 128 LEU cc_start: 0.8823 (tp) cc_final: 0.8377 (tp) REVERT: 1 149 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8523 (mm-30) REVERT: 1 156 MET cc_start: 0.8413 (mmm) cc_final: 0.8179 (mmm) REVERT: 1 202 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8005 (mm-30) REVERT: 1 221 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.7726 (tmm160) REVERT: 1 466 TYR cc_start: 0.7714 (t80) cc_final: 0.7272 (t80) REVERT: 1 467 MET cc_start: 0.8839 (mmm) cc_final: 0.8257 (mmm) REVERT: 1 480 SER cc_start: 0.9005 (t) cc_final: 0.8517 (p) REVERT: 1 483 HIS cc_start: 0.7030 (t-90) cc_final: 0.6779 (t-90) REVERT: 1 519 ILE cc_start: 0.8225 (mm) cc_final: 0.7927 (mm) REVERT: 1 547 ASN cc_start: 0.8573 (m-40) cc_final: 0.8141 (m-40) REVERT: 1 555 TYR cc_start: 0.7749 (m-80) cc_final: 0.7248 (m-80) REVERT: 1 562 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7739 (p0) REVERT: 1 569 GLN cc_start: 0.8373 (tp40) cc_final: 0.7585 (tm-30) REVERT: 1 570 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8476 (mp) REVERT: 1 585 MET cc_start: 0.7974 (mmp) cc_final: 0.7108 (mmp) REVERT: 1 633 GLU cc_start: 0.8276 (tp30) cc_final: 0.7712 (pp20) REVERT: 1 763 PHE cc_start: 0.7933 (t80) cc_final: 0.7390 (m-80) REVERT: 1 839 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (mp) REVERT: 1 846 MET cc_start: 0.8112 (mmm) cc_final: 0.7690 (tpp) REVERT: 1 958 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7592 (tp40) REVERT: 1 961 TYR cc_start: 0.7133 (t80) cc_final: 0.6914 (t80) REVERT: 1 964 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6372 (mt) REVERT: 1 977 MET cc_start: 0.8401 (tpt) cc_final: 0.8146 (tpt) REVERT: 1 1021 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7506 (ppp) REVERT: 1 1038 MET cc_start: 0.8386 (mmt) cc_final: 0.7713 (mmt) REVERT: 1 1084 PHE cc_start: 0.7809 (t80) cc_final: 0.7509 (t80) REVERT: 1 1091 ASP cc_start: 0.8596 (t0) cc_final: 0.8392 (t0) REVERT: 1 1105 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6385 (mt) REVERT: 1 1106 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7244 (mmp80) outliers start: 36 outliers final: 26 residues processed: 226 average time/residue: 0.1876 time to fit residues: 59.8564 Evaluate side-chains 232 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 119 CYS Chi-restraints excluded: chain 1 residue 137 ASP Chi-restraints excluded: chain 1 residue 145 THR Chi-restraints excluded: chain 1 residue 152 LEU Chi-restraints excluded: chain 1 residue 177 SER Chi-restraints excluded: chain 1 residue 207 LEU Chi-restraints excluded: chain 1 residue 224 LEU Chi-restraints excluded: chain 1 residue 254 SER Chi-restraints excluded: chain 1 residue 276 SER Chi-restraints excluded: chain 1 residue 281 ASN Chi-restraints excluded: chain 1 residue 328 THR Chi-restraints excluded: chain 1 residue 335 MET Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 377 MET Chi-restraints excluded: chain 1 residue 381 CYS Chi-restraints excluded: chain 1 residue 498 SER Chi-restraints excluded: chain 1 residue 562 ASP Chi-restraints excluded: chain 1 residue 570 LEU Chi-restraints excluded: chain 1 residue 574 LEU Chi-restraints excluded: chain 1 residue 705 HIS Chi-restraints excluded: chain 1 residue 790 VAL Chi-restraints excluded: chain 1 residue 839 LEU Chi-restraints excluded: chain 1 residue 847 VAL Chi-restraints excluded: chain 1 residue 903 THR Chi-restraints excluded: chain 1 residue 964 LEU Chi-restraints excluded: chain 1 residue 1021 MET Chi-restraints excluded: chain 1 residue 1035 SER Chi-restraints excluded: chain 1 residue 1059 LEU Chi-restraints excluded: chain 1 residue 1093 PHE Chi-restraints excluded: chain 1 residue 1105 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.0020 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 77 GLN 1 303 HIS 1 573 GLN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121452 restraints weight = 14201.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124603 restraints weight = 8187.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126785 restraints weight = 5453.329| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8566 Z= 0.181 Angle : 0.627 11.122 11585 Z= 0.308 Chirality : 0.040 0.188 1310 Planarity : 0.004 0.057 1473 Dihedral : 4.511 26.578 1184 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.71 % Allowed : 22.71 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1080 helix: 0.90 (0.21), residues: 616 sheet: 0.46 (0.89), residues: 40 loop : -1.30 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 154 HIS 0.004 0.001 HIS 1 738 PHE 0.017 0.002 PHE 1 219 TYR 0.026 0.001 TYR 1 751 ARG 0.004 0.000 ARG 1 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.05 seconds wall clock time: 39 minutes 58.92 seconds (2398.92 seconds total)