Starting phenix.real_space_refine on Wed Sep 25 18:17:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/09_2024/5xsy_6770.cif" } resolution = 4.0 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= 0.001 sd= 0.013 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 91 5.16 5 C 6982 2.51 5 N 1669 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9057 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 1110} Chain breaks: 6 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1371 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.08, per 1000 atoms: 0.85 Number of scatterers: 10634 At special positions: 0 Unit cell: (137.814, 131.124, 125.772, 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 91 16.00 O 1892 8.00 N 1669 7.00 C 6982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 324 " distance=2.00 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=1.98 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS A 725 " distance=2.15 Simple disulfide: pdb=" SG CYS A 757 " - pdb=" SG CYS A 766 " distance=1.95 Simple disulfide: pdb=" SG CYS A1158 " - pdb=" SG CYS A1178 " distance=2.38 Simple disulfide: pdb=" SG CYS A1522 " - pdb=" SG CYS A1537 " distance=1.94 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 47 " distance=1.96 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 124 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG C 1 " - " ASN A 317 " " NAG D 1 " - " ASN A1174 " " NAG E 1 " - " ASN A1160 " " NAG F 1 " - " ASN B 113 " " NAG G 1 " - " ASN B 117 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 4 sheets defined 71.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.645A pdb=" N ALA A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.638A pdb=" N PHE A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 169 removed outlier: 3.588A pdb=" N GLU A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.622A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 190 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.603A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 264 removed outlier: 4.206A pdb=" N ILE A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 242 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.950A pdb=" N THR A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.012A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.700A pdb=" N MET A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.722A pdb=" N ILE A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 399 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 431 removed outlier: 3.593A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.801A pdb=" N VAL A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 removed outlier: 4.035A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 618 removed outlier: 3.926A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 628 removed outlier: 4.051A pdb=" N GLN A 628 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 648 removed outlier: 3.685A pdb=" N SER A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.587A pdb=" N LEU A 656 " --> pdb=" O MET A 653 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 657 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 659 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 660 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 662 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.715A pdb=" N LEU A 667 " --> pdb=" O ARG A 663 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 673 through 684 removed outlier: 3.801A pdb=" N LYS A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 717 removed outlier: 3.801A pdb=" N THR A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 694 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 710 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS A 712 " --> pdb=" O GLN A 708 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 734 through 747 removed outlier: 3.623A pdb=" N SER A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 761 removed outlier: 4.428A pdb=" N ASP A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 759 " --> pdb=" O TRP A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 792 removed outlier: 3.758A pdb=" N CYS A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 767 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 999 removed outlier: 3.570A pdb=" N ASN A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 997 " --> pdb=" O CYS A 993 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1018 Processing helix chain 'A' and resid 1019 through 1020 No H-bonds generated for 'chain 'A' and resid 1019 through 1020' Processing helix chain 'A' and resid 1021 through 1026 Processing helix chain 'A' and resid 1028 through 1064 removed outlier: 3.515A pdb=" N ASP A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1040 " --> pdb=" O TYR A1036 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A1053 " --> pdb=" O MET A1049 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N LYS A1059 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A1060 " --> pdb=" O TYR A1056 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A1062 " --> pdb=" O PHE A1058 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A1064 " --> pdb=" O ARG A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1082 removed outlier: 4.107A pdb=" N ASP A1070 " --> pdb=" O TRP A1066 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A1071 " --> pdb=" O CYS A1067 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A1074 " --> pdb=" O ASP A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.922A pdb=" N ARG A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1112 removed outlier: 4.043A pdb=" N ARG A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1152 removed outlier: 3.686A pdb=" N LYS A1116 " --> pdb=" O PHE A1112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A1117 " --> pdb=" O GLU A1113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A1118 " --> pdb=" O GLY A1114 " (cutoff:3.500A) Proline residue: A1127 - end of helix removed outlier: 3.725A pdb=" N ASN A1131 " --> pdb=" O PRO A1127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A1142 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A1143 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A1149 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 4.012A pdb=" N LEU A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1209 Processing helix chain 'A' and resid 1214 through 1224 removed outlier: 3.837A pdb=" N ILE A1218 " --> pdb=" O GLY A1214 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1240 through 1251 removed outlier: 4.355A pdb=" N PHE A1244 " --> pdb=" O MET A1240 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1273 removed outlier: 4.006A pdb=" N ASP A1265 " --> pdb=" O GLY A1261 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A1271 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1272 " --> pdb=" O ASN A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1298 removed outlier: 3.844A pdb=" N LYS A1287 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A1294 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A1295 " --> pdb=" O ALA A1291 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A1296 " --> pdb=" O MET A1292 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1321 Processing helix chain 'A' and resid 1321 through 1339 removed outlier: 3.720A pdb=" N ASP A1325 " --> pdb=" O GLN A1321 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A1326 " --> pdb=" O PRO A1322 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A1327 " --> pdb=" O PHE A1323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1329 " --> pdb=" O ASP A1325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1342 No H-bonds generated for 'chain 'A' and resid 1340 through 1342' Processing helix chain 'A' and resid 1347 through 1381 removed outlier: 3.531A pdb=" N PHE A1365 " --> pdb=" O PHE A1361 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1406 removed outlier: 3.923A pdb=" N VAL A1394 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A1398 " --> pdb=" O VAL A1394 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A1400 " --> pdb=" O SER A1396 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1401 " --> pdb=" O ILE A1397 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1403 " --> pdb=" O GLY A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1421 removed outlier: 3.796A pdb=" N VAL A1418 " --> pdb=" O THR A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1429 removed outlier: 3.562A pdb=" N ARG A1426 " --> pdb=" O ARG A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1435 removed outlier: 3.515A pdb=" N ALA A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A1435 " --> pdb=" O ILE A1431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1430 through 1435' Processing helix chain 'A' and resid 1435 through 1447 removed outlier: 4.192A pdb=" N LEU A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A1444 " --> pdb=" O LEU A1440 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A1445 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1474 removed outlier: 3.687A pdb=" N ILE A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A1455 " --> pdb=" O LEU A1451 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A1472 " --> pdb=" O PHE A1468 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A1474 " --> pdb=" O MET A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1503 removed outlier: 3.552A pdb=" N SER A1494 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A1495 " --> pdb=" O PHE A1491 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A1496 " --> pdb=" O GLY A1492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A1500 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A1501 " --> pdb=" O CYS A1497 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A1503 " --> pdb=" O PHE A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1516 removed outlier: 3.518A pdb=" N LEU A1512 " --> pdb=" O ASP A1508 " (cutoff:3.500A) Proline residue: A1513 - end of helix Processing helix chain 'A' and resid 1539 through 1570 removed outlier: 3.719A pdb=" N THR A1545 " --> pdb=" O GLY A1541 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1546 " --> pdb=" O LYS A1542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1552 " --> pdb=" O CYS A1548 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1559 " --> pdb=" O PHE A1555 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU A1568 " --> pdb=" O ALA A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1578 removed outlier: 4.148A pdb=" N GLU A1575 " --> pdb=" O GLY A1571 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 160 through 191 removed outlier: 3.876A pdb=" N TYR B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 273 Processing sheet with id=AA2, first strand: chain 'A' and resid 1157 through 1160 Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.355A pdb=" N ALA B 34 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 126 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 143 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 75 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 45 552 hydrogen bonds defined for protein. 1593 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: 3.50 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1903 1.32 - 1.45: 2916 1.45 - 1.57: 5904 1.57 - 1.69: 1 1.69 - 1.81: 150 Bond restraints: 10874 Sorted by residual: bond pdb=" CA GLU B 136 " pdb=" C GLU B 136 " ideal model delta sigma weight residual 1.523 1.681 -0.159 1.28e-02 6.10e+03 1.54e+02 bond pdb=" C GLY A1518 " pdb=" N PRO A1519 " ideal model delta sigma weight residual 1.329 1.403 -0.073 1.18e-02 7.18e+03 3.87e+01 bond pdb=" N PRO A1520 " pdb=" CD PRO A1520 " ideal model delta sigma weight residual 1.474 1.554 -0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" N PRO A 183 " pdb=" CD PRO A 183 " ideal model delta sigma weight residual 1.473 1.550 -0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" N PRO A1519 " pdb=" CD PRO A1519 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.63: 14585 5.63 - 11.26: 134 11.26 - 16.90: 19 16.90 - 22.53: 3 22.53 - 28.16: 4 Bond angle restraints: 14745 Sorted by residual: angle pdb=" N LEU B 130 " pdb=" CA LEU B 130 " pdb=" C LEU B 130 " ideal model delta sigma weight residual 109.46 81.30 28.16 1.66e+00 3.63e-01 2.88e+02 angle pdb=" C TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta sigma weight residual 109.48 83.04 26.44 1.68e+00 3.54e-01 2.48e+02 angle pdb=" C LEU B 130 " pdb=" CA LEU B 130 " pdb=" CB LEU B 130 " ideal model delta sigma weight residual 109.80 134.63 -24.83 1.64e+00 3.72e-01 2.29e+02 angle pdb=" C SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta sigma weight residual 109.38 82.35 27.03 2.03e+00 2.43e-01 1.77e+02 angle pdb=" C MET B 83 " pdb=" CA MET B 83 " pdb=" CB MET B 83 " ideal model delta sigma weight residual 110.19 92.25 17.94 1.62e+00 3.81e-01 1.23e+02 ... (remaining 14740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 6041 23.10 - 46.21: 355 46.21 - 69.31: 100 69.31 - 92.41: 35 92.41 - 115.52: 29 Dihedral angle restraints: 6560 sinusoidal: 2729 harmonic: 3831 Sorted by residual: dihedral pdb=" C SER B 76 " pdb=" N SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta harmonic sigma weight residual -122.60 -94.64 -27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR B 110 " pdb=" N TYR B 110 " pdb=" CA TYR B 110 " pdb=" CB TYR B 110 " ideal model delta harmonic sigma weight residual -122.60 -95.89 -26.71 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -168.70 82.70 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 6557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1482 0.095 - 0.190: 217 0.190 - 0.285: 39 0.285 - 0.380: 8 0.380 - 0.475: 5 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA ALA A1573 " pdb=" N ALA A1573 " pdb=" C ALA A1573 " pdb=" CB ALA A1573 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA GLU B 136 " pdb=" N GLU B 136 " pdb=" C GLU B 136 " pdb=" CB GLU B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA GLU A 586 " pdb=" N GLU A 586 " pdb=" C GLU A 586 " pdb=" CB GLU A 586 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 1748 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -1.075 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG A 213 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 268 " -1.014 9.50e-02 1.11e+02 4.55e-01 1.25e+02 pdb=" NE ARG A 268 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 268 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 268 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 268 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 336 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO A 337 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.064 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 27 2.37 - 3.00: 6081 3.00 - 3.63: 15491 3.63 - 4.27: 22949 4.27 - 4.90: 36672 Nonbonded interactions: 81220 Sorted by model distance: nonbonded pdb=" CG1 VAL A1016 " pdb=" CD1 LEU A1034 " model vdw 1.735 3.880 nonbonded pdb=" O GLN A1346 " pdb=" OG SER A1347 " model vdw 1.915 3.040 nonbonded pdb=" O LEU A 620 " pdb=" O ASP A 621 " model vdw 1.993 3.040 nonbonded pdb=" O THR A 629 " pdb=" CG2 ILE A 632 " model vdw 2.137 3.460 nonbonded pdb=" O ASP A1483 " pdb=" OD1 ASP A1484 " model vdw 2.176 3.040 ... (remaining 81215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.250 Process input model: 30.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.110 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:4.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.011 0.159 10874 Z= 0.703 Angle : 1.554 28.161 14745 Z= 0.936 Chirality : 0.077 0.475 1751 Planarity : 0.017 0.482 1789 Dihedral : 18.877 115.517 4062 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 31.93 Ramachandran Plot: Outliers : 1.54 % Allowed : 6.64 % Favored : 91.82 % Rotamer: Outliers : 7.45 % Allowed : 8.35 % Favored : 84.20 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.53 (0.20), residues: 1296 helix: -1.95 (0.17), residues: 784 sheet: -2.65 (0.52), residues: 68 loop : -2.74 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A1215 HIS 0.022 0.004 HIS A 588 PHE 0.031 0.003 PHE B 63 TYR 0.035 0.004 TYR A 714 ARG 0.011 0.001 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 428 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5324 (ptt180) REVERT: A 129 MET cc_start: 0.8068 (ttm) cc_final: 0.7513 (tmm) REVERT: A 133 PHE cc_start: 0.7602 (t80) cc_final: 0.7376 (t80) REVERT: A 139 MET cc_start: 0.8688 (tpp) cc_final: 0.8260 (mtt) REVERT: A 194 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6163 (mmp) REVERT: A 232 ARG cc_start: 0.7448 (ttt180) cc_final: 0.6818 (tpt170) REVERT: A 250 PHE cc_start: 0.8270 (t80) cc_final: 0.7236 (m-10) REVERT: A 255 PHE cc_start: 0.9090 (m-80) cc_final: 0.8887 (m-80) REVERT: A 266 ASN cc_start: 0.9021 (m-40) cc_final: 0.8093 (m110) REVERT: A 268 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7644 (ttm170) REVERT: A 298 GLU cc_start: 0.9374 (tt0) cc_final: 0.8654 (pt0) REVERT: A 372 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7373 (ttm170) REVERT: A 405 TYR cc_start: 0.6925 (m-10) cc_final: 0.6694 (m-10) REVERT: A 590 MET cc_start: 0.7093 (mtp) cc_final: 0.6790 (mmm) REVERT: A 647 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2826 (tp) REVERT: A 679 LYS cc_start: 0.8843 (tttt) cc_final: 0.8530 (tppt) REVERT: A 717 TYR cc_start: 0.8402 (m-80) cc_final: 0.8169 (m-10) REVERT: A 725 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6974 (t) REVERT: A 726 GLU cc_start: 0.8725 (tt0) cc_final: 0.7514 (tm-30) REVERT: A 732 MET cc_start: 0.8640 (mmt) cc_final: 0.8430 (mmm) REVERT: A 771 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7011 (ttt) REVERT: A 999 HIS cc_start: 0.7853 (t-90) cc_final: 0.7477 (t-170) REVERT: A 1002 PHE cc_start: 0.8329 (t80) cc_final: 0.8115 (t80) REVERT: A 1059 LYS cc_start: 0.7619 (tttp) cc_final: 0.7181 (mptt) REVERT: A 1064 ASP cc_start: 0.7845 (m-30) cc_final: 0.7551 (t0) REVERT: A 1067 CYS cc_start: 0.8568 (m) cc_final: 0.8228 (m) REVERT: A 1071 PHE cc_start: 0.8683 (t80) cc_final: 0.8460 (t80) REVERT: A 1110 SER cc_start: 0.8704 (t) cc_final: 0.8450 (m) REVERT: A 1120 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7895 (ttm110) REVERT: A 1165 GLU cc_start: 0.8720 (tt0) cc_final: 0.8119 (mm-30) REVERT: A 1192 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8023 (tm) REVERT: A 1231 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 1240 MET cc_start: 0.9257 (mmp) cc_final: 0.8767 (tpp) REVERT: A 1288 TYR cc_start: 0.8283 (m-10) cc_final: 0.7850 (m-10) REVERT: A 1294 LYS cc_start: 0.6906 (mttt) cc_final: 0.6474 (mmmt) REVERT: A 1325 ASP cc_start: 0.8607 (m-30) cc_final: 0.8368 (t0) REVERT: A 1326 ILE cc_start: 0.8148 (mt) cc_final: 0.7773 (mt) REVERT: A 1329 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: A 1340 MET cc_start: 0.9063 (mtp) cc_final: 0.8600 (ttt) REVERT: A 1377 ARG cc_start: 0.3999 (tpt170) cc_final: 0.3646 (mmt-90) REVERT: A 1419 ILE cc_start: 0.9035 (mm) cc_final: 0.8788 (mm) REVERT: A 1446 MET cc_start: 0.8183 (ttt) cc_final: 0.7973 (ttm) REVERT: A 1468 PHE cc_start: 0.8617 (t80) cc_final: 0.8346 (t80) REVERT: A 1523 ASP cc_start: 0.7661 (m-30) cc_final: 0.7190 (t70) REVERT: B 27 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: B 28 VAL cc_start: 0.8886 (p) cc_final: 0.8597 (p) REVERT: B 38 HIS cc_start: 0.8160 (t-90) cc_final: 0.7835 (t-90) REVERT: B 62 TRP cc_start: 0.8178 (m100) cc_final: 0.7404 (m-10) REVERT: B 72 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (t) REVERT: B 75 TYR cc_start: 0.8686 (t80) cc_final: 0.8181 (t80) REVERT: B 81 THR cc_start: 0.9063 (m) cc_final: 0.8846 (m) REVERT: B 94 ASN cc_start: 0.8316 (t0) cc_final: 0.7842 (t0) REVERT: B 114 VAL cc_start: 0.9382 (t) cc_final: 0.8998 (p) REVERT: B 121 THR cc_start: 0.7770 (m) cc_final: 0.7525 (m) REVERT: B 125 TYR cc_start: 0.7672 (t80) cc_final: 0.6948 (t80) REVERT: B 155 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8156 (mtt180) REVERT: B 163 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: B 165 MET cc_start: 0.8112 (mmm) cc_final: 0.7348 (tmm) REVERT: B 177 LEU cc_start: 0.8981 (mt) cc_final: 0.8747 (mt) REVERT: B 183 TYR cc_start: 0.8035 (t80) cc_final: 0.7561 (t80) REVERT: B 194 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7273 (mp0) outliers start: 83 outliers final: 27 residues processed: 477 average time/residue: 0.2262 time to fit residues: 150.2155 Evaluate side-chains 350 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 310 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1329 MET Chi-restraints excluded: chain A residue 1364 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 346 ASN A 560 HIS A 628 GLN A 631 ASN A 690 ASN A1270 GLN B 73 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10874 Z= 0.264 Angle : 0.854 11.658 14745 Z= 0.447 Chirality : 0.048 0.252 1751 Planarity : 0.006 0.087 1789 Dihedral : 15.234 89.195 1824 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.63 % Favored : 93.75 % Rotamer: Outliers : 6.55 % Allowed : 17.59 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.21), residues: 1296 helix: -1.25 (0.16), residues: 841 sheet: -2.51 (0.57), residues: 66 loop : -2.71 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1215 HIS 0.008 0.002 HIS A 588 PHE 0.023 0.002 PHE A 177 TYR 0.025 0.002 TYR B 110 ARG 0.006 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 364 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6646 (mtt90) cc_final: 0.5148 (ptt180) REVERT: A 129 MET cc_start: 0.7879 (ttm) cc_final: 0.7305 (tmm) REVERT: A 133 PHE cc_start: 0.7127 (t80) cc_final: 0.6839 (t80) REVERT: A 139 MET cc_start: 0.8734 (tpp) cc_final: 0.8176 (mtt) REVERT: A 232 ARG cc_start: 0.7054 (ttt180) cc_final: 0.6439 (tpt90) REVERT: A 240 GLN cc_start: 0.7502 (tp40) cc_final: 0.7150 (tm-30) REVERT: A 250 PHE cc_start: 0.7772 (t80) cc_final: 0.6858 (m-10) REVERT: A 255 PHE cc_start: 0.9269 (m-80) cc_final: 0.9059 (m-10) REVERT: A 266 ASN cc_start: 0.8979 (m-40) cc_final: 0.8096 (m110) REVERT: A 300 GLU cc_start: 0.9216 (tt0) cc_final: 0.8993 (tt0) REVERT: A 335 ARG cc_start: 0.9027 (tmm-80) cc_final: 0.8804 (ptm160) REVERT: A 382 PHE cc_start: 0.8796 (m-10) cc_final: 0.8593 (m-80) REVERT: A 407 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7475 (tt0) REVERT: A 595 GLN cc_start: 0.8311 (mt0) cc_final: 0.8001 (mt0) REVERT: A 625 TYR cc_start: 0.4961 (t80) cc_final: 0.4640 (t80) REVERT: A 634 ASP cc_start: 0.8704 (m-30) cc_final: 0.7542 (m-30) REVERT: A 660 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7894 (ttp-110) REVERT: A 690 ASN cc_start: 0.8950 (t0) cc_final: 0.8610 (t0) REVERT: A 726 GLU cc_start: 0.8360 (tt0) cc_final: 0.7916 (tm-30) REVERT: A 771 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6623 (ttt) REVERT: A 1059 LYS cc_start: 0.7353 (tttp) cc_final: 0.6977 (mptt) REVERT: A 1061 TYR cc_start: 0.7986 (t80) cc_final: 0.7037 (t80) REVERT: A 1064 ASP cc_start: 0.7932 (m-30) cc_final: 0.7551 (t0) REVERT: A 1067 CYS cc_start: 0.8651 (m) cc_final: 0.8115 (m) REVERT: A 1110 SER cc_start: 0.8779 (t) cc_final: 0.8499 (m) REVERT: A 1120 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7912 (ttm110) REVERT: A 1156 TYR cc_start: 0.8474 (m-80) cc_final: 0.8253 (m-80) REVERT: A 1165 GLU cc_start: 0.8662 (tt0) cc_final: 0.8047 (mm-30) REVERT: A 1191 ASN cc_start: 0.8877 (t0) cc_final: 0.8620 (t0) REVERT: A 1203 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8524 (t80) REVERT: A 1231 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 1240 MET cc_start: 0.8680 (mmp) cc_final: 0.8187 (tpp) REVERT: A 1289 TYR cc_start: 0.8194 (t80) cc_final: 0.7945 (t80) REVERT: A 1294 LYS cc_start: 0.6967 (mttt) cc_final: 0.6762 (mmmt) REVERT: A 1325 ASP cc_start: 0.8494 (m-30) cc_final: 0.8172 (t0) REVERT: A 1326 ILE cc_start: 0.7971 (mt) cc_final: 0.7600 (mt) REVERT: A 1329 MET cc_start: 0.8261 (mmt) cc_final: 0.7861 (tmm) REVERT: A 1377 ARG cc_start: 0.4247 (tpt170) cc_final: 0.3655 (mmt-90) REVERT: A 1446 MET cc_start: 0.8056 (ttt) cc_final: 0.7724 (ttm) REVERT: A 1468 PHE cc_start: 0.8447 (t80) cc_final: 0.8238 (t80) REVERT: B 27 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: B 28 VAL cc_start: 0.8888 (p) cc_final: 0.8612 (p) REVERT: B 62 TRP cc_start: 0.8150 (m100) cc_final: 0.7534 (m-10) REVERT: B 83 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8846 (mtp) REVERT: B 94 ASN cc_start: 0.8752 (t0) cc_final: 0.8510 (t0) REVERT: B 96 MET cc_start: 0.7992 (mmm) cc_final: 0.7706 (ttm) REVERT: B 148 ASN cc_start: 0.8843 (t0) cc_final: 0.8308 (p0) REVERT: B 155 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8047 (mmt90) REVERT: B 163 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: B 165 MET cc_start: 0.8027 (mmm) cc_final: 0.7414 (tmm) REVERT: B 167 TYR cc_start: 0.8148 (m-80) cc_final: 0.7835 (m-80) REVERT: B 177 LEU cc_start: 0.8968 (mt) cc_final: 0.8742 (mt) outliers start: 73 outliers final: 31 residues processed: 402 average time/residue: 0.2126 time to fit residues: 123.2876 Evaluate side-chains 338 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 300 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1359 VAL Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1537 CYS Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN B 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10874 Z= 0.238 Angle : 0.750 9.415 14745 Z= 0.389 Chirality : 0.045 0.237 1751 Planarity : 0.005 0.099 1789 Dihedral : 11.893 89.960 1784 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 6.73 % Allowed : 21.01 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1296 helix: -0.74 (0.17), residues: 842 sheet: -2.18 (0.56), residues: 64 loop : -2.52 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1507 HIS 0.018 0.003 HIS B 73 PHE 0.020 0.002 PHE B 102 TYR 0.023 0.002 TYR B 110 ARG 0.009 0.001 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 322 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6493 (mtt90) cc_final: 0.5074 (ptt-90) REVERT: A 129 MET cc_start: 0.8087 (ttm) cc_final: 0.7463 (tmm) REVERT: A 139 MET cc_start: 0.8759 (tpp) cc_final: 0.8281 (mtt) REVERT: A 166 LYS cc_start: 0.8773 (mttt) cc_final: 0.8352 (mtpt) REVERT: A 240 GLN cc_start: 0.7480 (tp40) cc_final: 0.7272 (tm-30) REVERT: A 250 PHE cc_start: 0.7731 (t80) cc_final: 0.6995 (m-10) REVERT: A 264 MET cc_start: 0.9161 (ttm) cc_final: 0.8844 (tpp) REVERT: A 266 ASN cc_start: 0.8996 (m-40) cc_final: 0.8279 (m-40) REVERT: A 305 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8420 (p90) REVERT: A 326 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8576 (mp0) REVERT: A 382 PHE cc_start: 0.8846 (m-10) cc_final: 0.8464 (m-80) REVERT: A 391 PHE cc_start: 0.8316 (t80) cc_final: 0.8042 (t80) REVERT: A 590 MET cc_start: 0.5967 (mmm) cc_final: 0.5001 (mmm) REVERT: A 595 GLN cc_start: 0.8405 (mt0) cc_final: 0.8040 (mt0) REVERT: A 726 GLU cc_start: 0.8268 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 771 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6526 (ttt) REVERT: A 1049 MET cc_start: 0.8186 (tmm) cc_final: 0.7886 (tmm) REVERT: A 1059 LYS cc_start: 0.7365 (tttp) cc_final: 0.7150 (mptt) REVERT: A 1061 TYR cc_start: 0.7739 (t80) cc_final: 0.6753 (t80) REVERT: A 1067 CYS cc_start: 0.8517 (m) cc_final: 0.8026 (m) REVERT: A 1110 SER cc_start: 0.8594 (t) cc_final: 0.8290 (m) REVERT: A 1120 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8096 (ttm110) REVERT: A 1165 GLU cc_start: 0.8687 (tt0) cc_final: 0.8128 (mm-30) REVERT: A 1194 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8759 (m) REVERT: A 1231 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 1292 MET cc_start: 0.6156 (mmp) cc_final: 0.5026 (mtt) REVERT: A 1325 ASP cc_start: 0.8437 (m-30) cc_final: 0.8136 (t0) REVERT: A 1329 MET cc_start: 0.8306 (mmt) cc_final: 0.7882 (ppp) REVERT: A 1336 MET cc_start: 0.8854 (ttt) cc_final: 0.8404 (tmm) REVERT: A 1372 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8182 (mtmt) REVERT: A 1377 ARG cc_start: 0.4058 (tpt170) cc_final: 0.3422 (mmt-90) REVERT: A 1446 MET cc_start: 0.8112 (ttt) cc_final: 0.7882 (ttm) REVERT: A 1508 ASP cc_start: 0.8964 (p0) cc_final: 0.8754 (p0) REVERT: B 28 VAL cc_start: 0.8955 (p) cc_final: 0.8726 (p) REVERT: B 62 TRP cc_start: 0.8373 (m100) cc_final: 0.7507 (m-10) REVERT: B 94 ASN cc_start: 0.8784 (t0) cc_final: 0.8522 (t0) REVERT: B 96 MET cc_start: 0.8044 (mmm) cc_final: 0.7525 (ttm) REVERT: B 148 ASN cc_start: 0.8853 (t0) cc_final: 0.8423 (p0) REVERT: B 163 GLU cc_start: 0.8582 (tt0) cc_final: 0.7914 (tm-30) REVERT: B 165 MET cc_start: 0.8033 (mmm) cc_final: 0.7461 (tmm) REVERT: B 167 TYR cc_start: 0.8054 (m-80) cc_final: 0.7579 (m-80) REVERT: B 173 LEU cc_start: 0.8672 (mt) cc_final: 0.8467 (mt) REVERT: B 177 LEU cc_start: 0.8753 (mt) cc_final: 0.8454 (mt) outliers start: 75 outliers final: 44 residues processed: 365 average time/residue: 0.2014 time to fit residues: 107.4210 Evaluate side-chains 335 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 287 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 113 optimal weight: 0.0020 chunk 34 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 HIS A1335 ASN B 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10874 Z= 0.189 Angle : 0.706 11.782 14745 Z= 0.363 Chirality : 0.043 0.237 1751 Planarity : 0.005 0.109 1789 Dihedral : 9.953 86.859 1768 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.79 % Favored : 93.67 % Rotamer: Outliers : 5.48 % Allowed : 23.97 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -1.71 (0.22), residues: 1296 helix: -0.37 (0.17), residues: 840 sheet: -1.74 (0.62), residues: 56 loop : -2.54 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1507 HIS 0.006 0.001 HIS A 588 PHE 0.020 0.001 PHE B 102 TYR 0.020 0.001 TYR A 625 ARG 0.007 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 326 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6477 (mtt90) cc_final: 0.5049 (ptt-90) REVERT: A 129 MET cc_start: 0.7964 (ttm) cc_final: 0.7371 (tmm) REVERT: A 133 PHE cc_start: 0.6902 (t80) cc_final: 0.6699 (t80) REVERT: A 139 MET cc_start: 0.8837 (tpp) cc_final: 0.8314 (mtt) REVERT: A 166 LYS cc_start: 0.8804 (mttt) cc_final: 0.8555 (mmmt) REVERT: A 250 PHE cc_start: 0.7784 (t80) cc_final: 0.6981 (m-10) REVERT: A 264 MET cc_start: 0.9150 (ttm) cc_final: 0.8853 (tpp) REVERT: A 266 ASN cc_start: 0.8963 (m-40) cc_final: 0.8258 (m-40) REVERT: A 326 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8588 (mp0) REVERT: A 391 PHE cc_start: 0.8261 (t80) cc_final: 0.8035 (t80) REVERT: A 590 MET cc_start: 0.5997 (mmm) cc_final: 0.5041 (mmm) REVERT: A 595 GLN cc_start: 0.8371 (mt0) cc_final: 0.7978 (mt0) REVERT: A 605 PHE cc_start: 0.8378 (m-80) cc_final: 0.8157 (m-80) REVERT: A 625 TYR cc_start: 0.3973 (t80) cc_final: 0.3760 (t80) REVERT: A 726 GLU cc_start: 0.8320 (tt0) cc_final: 0.8048 (tm-30) REVERT: A 771 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.6780 (ttt) REVERT: A 1049 MET cc_start: 0.8173 (tmm) cc_final: 0.7832 (tmm) REVERT: A 1059 LYS cc_start: 0.7446 (tttp) cc_final: 0.7043 (mptt) REVERT: A 1067 CYS cc_start: 0.8399 (m) cc_final: 0.8171 (m) REVERT: A 1110 SER cc_start: 0.8590 (t) cc_final: 0.8284 (m) REVERT: A 1120 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8028 (ttm110) REVERT: A 1163 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 1165 GLU cc_start: 0.8661 (tt0) cc_final: 0.8220 (mm-30) REVERT: A 1231 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 1292 MET cc_start: 0.6207 (mmp) cc_final: 0.5156 (mtt) REVERT: A 1325 ASP cc_start: 0.8435 (m-30) cc_final: 0.8182 (t0) REVERT: A 1329 MET cc_start: 0.8217 (mmt) cc_final: 0.7766 (tmm) REVERT: A 1336 MET cc_start: 0.8825 (ttt) cc_final: 0.8369 (tmm) REVERT: A 1372 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8682 (mtmt) REVERT: A 1377 ARG cc_start: 0.2965 (tpt170) cc_final: 0.2339 (mmt-90) REVERT: A 1446 MET cc_start: 0.8281 (ttt) cc_final: 0.8012 (ttm) REVERT: A 1475 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.6492 (p90) REVERT: A 1515 LEU cc_start: 0.8390 (mt) cc_final: 0.8047 (mt) REVERT: B 27 GLU cc_start: 0.8768 (pt0) cc_final: 0.8530 (pt0) REVERT: B 28 VAL cc_start: 0.9164 (p) cc_final: 0.8947 (p) REVERT: B 62 TRP cc_start: 0.8425 (m100) cc_final: 0.7655 (m-10) REVERT: B 94 ASN cc_start: 0.8800 (t0) cc_final: 0.8511 (t0) REVERT: B 96 MET cc_start: 0.8008 (mmm) cc_final: 0.7793 (ttm) REVERT: B 163 GLU cc_start: 0.8406 (tt0) cc_final: 0.7822 (tm-30) REVERT: B 165 MET cc_start: 0.8081 (mmm) cc_final: 0.7496 (tmm) REVERT: B 167 TYR cc_start: 0.8110 (m-80) cc_final: 0.7544 (m-80) REVERT: B 177 LEU cc_start: 0.8638 (mt) cc_final: 0.8396 (mt) outliers start: 61 outliers final: 43 residues processed: 367 average time/residue: 0.2274 time to fit residues: 126.2766 Evaluate side-chains 344 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 297 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 0.0070 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN B 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10874 Z= 0.191 Angle : 0.684 9.295 14745 Z= 0.355 Chirality : 0.042 0.215 1751 Planarity : 0.004 0.097 1789 Dihedral : 8.971 87.131 1763 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.71 % Favored : 93.75 % Rotamer: Outliers : 5.75 % Allowed : 24.24 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1296 helix: -0.12 (0.17), residues: 842 sheet: -1.72 (0.58), residues: 62 loop : -2.49 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1507 HIS 0.013 0.002 HIS B 73 PHE 0.021 0.001 PHE B 102 TYR 0.018 0.001 TYR B 125 ARG 0.005 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6477 (mtt90) cc_final: 0.5087 (ptt180) REVERT: A 129 MET cc_start: 0.7980 (ttm) cc_final: 0.7395 (tmm) REVERT: A 139 MET cc_start: 0.8643 (tpp) cc_final: 0.8351 (mtt) REVERT: A 166 LYS cc_start: 0.8887 (mttt) cc_final: 0.8516 (mtmt) REVERT: A 264 MET cc_start: 0.9172 (ttm) cc_final: 0.8952 (tpp) REVERT: A 266 ASN cc_start: 0.8969 (m-40) cc_final: 0.8202 (m-40) REVERT: A 343 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7608 (p0) REVERT: A 391 PHE cc_start: 0.8388 (t80) cc_final: 0.8163 (t80) REVERT: A 563 MET cc_start: 0.7202 (tmm) cc_final: 0.6973 (tmm) REVERT: A 590 MET cc_start: 0.6000 (mmm) cc_final: 0.5004 (mmm) REVERT: A 595 GLN cc_start: 0.8319 (mt0) cc_final: 0.7893 (mt0) REVERT: A 605 PHE cc_start: 0.8406 (m-80) cc_final: 0.7967 (m-10) REVERT: A 608 ILE cc_start: 0.8550 (mm) cc_final: 0.8274 (mt) REVERT: A 625 TYR cc_start: 0.4392 (t80) cc_final: 0.4068 (t80) REVERT: A 726 GLU cc_start: 0.8226 (tt0) cc_final: 0.7980 (tm-30) REVERT: A 771 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6751 (ttt) REVERT: A 1049 MET cc_start: 0.8127 (tmm) cc_final: 0.7844 (tmm) REVERT: A 1059 LYS cc_start: 0.7417 (tttp) cc_final: 0.7028 (mptt) REVERT: A 1067 CYS cc_start: 0.8334 (m) cc_final: 0.8090 (m) REVERT: A 1110 SER cc_start: 0.8607 (t) cc_final: 0.8378 (m) REVERT: A 1120 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8018 (ttm110) REVERT: A 1163 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 1165 GLU cc_start: 0.8706 (tt0) cc_final: 0.8069 (mm-30) REVERT: A 1240 MET cc_start: 0.9024 (mmp) cc_final: 0.8642 (tpp) REVERT: A 1281 MET cc_start: 0.8009 (mpp) cc_final: 0.7698 (mpp) REVERT: A 1292 MET cc_start: 0.6248 (mmp) cc_final: 0.5239 (mtt) REVERT: A 1325 ASP cc_start: 0.8401 (m-30) cc_final: 0.8167 (t0) REVERT: A 1329 MET cc_start: 0.8191 (mmt) cc_final: 0.7746 (tmm) REVERT: A 1336 MET cc_start: 0.8832 (ttt) cc_final: 0.8412 (tmm) REVERT: A 1372 LYS cc_start: 0.9026 (mmtp) cc_final: 0.8677 (mtmt) REVERT: A 1446 MET cc_start: 0.8148 (ttt) cc_final: 0.7936 (ttm) REVERT: A 1475 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6391 (p90) REVERT: A 1485 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 1515 LEU cc_start: 0.8375 (mt) cc_final: 0.8061 (mt) REVERT: B 27 GLU cc_start: 0.8845 (pt0) cc_final: 0.8615 (pt0) REVERT: B 28 VAL cc_start: 0.9168 (p) cc_final: 0.8950 (p) REVERT: B 50 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7930 (tpt90) REVERT: B 62 TRP cc_start: 0.8445 (m100) cc_final: 0.7738 (m-10) REVERT: B 70 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6458 (tp30) REVERT: B 81 THR cc_start: 0.8902 (m) cc_final: 0.8700 (t) REVERT: B 96 MET cc_start: 0.7803 (mmm) cc_final: 0.7389 (ttm) REVERT: B 163 GLU cc_start: 0.8404 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 165 MET cc_start: 0.8089 (mmm) cc_final: 0.7487 (tmm) REVERT: B 167 TYR cc_start: 0.8062 (m-80) cc_final: 0.7416 (m-80) REVERT: B 173 LEU cc_start: 0.8569 (mt) cc_final: 0.8331 (mt) REVERT: B 177 LEU cc_start: 0.8626 (mt) cc_final: 0.8399 (mt) outliers start: 64 outliers final: 44 residues processed: 352 average time/residue: 0.1851 time to fit residues: 96.3513 Evaluate side-chains 342 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10874 Z= 0.195 Angle : 0.708 12.435 14745 Z= 0.359 Chirality : 0.043 0.227 1751 Planarity : 0.004 0.091 1789 Dihedral : 8.338 85.889 1763 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.63 % Favored : 93.83 % Rotamer: Outliers : 6.73 % Allowed : 23.70 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % 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: -1.17 (0.23), residues: 1296 helix: 0.09 (0.17), residues: 842 sheet: -1.48 (0.61), residues: 62 loop : -2.45 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1507 HIS 0.004 0.001 HIS A 588 PHE 0.022 0.001 PHE B 102 TYR 0.013 0.001 TYR B 125 ARG 0.008 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 299 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6426 (mtt90) cc_final: 0.5025 (ptt180) REVERT: A 129 MET cc_start: 0.7908 (ttm) cc_final: 0.7330 (tmm) REVERT: A 166 LYS cc_start: 0.8868 (mttt) cc_final: 0.8658 (mmmt) REVERT: A 228 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: A 266 ASN cc_start: 0.8949 (m-40) cc_final: 0.8196 (m-40) REVERT: A 343 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 391 PHE cc_start: 0.8423 (t80) cc_final: 0.8182 (t80) REVERT: A 563 MET cc_start: 0.7190 (tmm) cc_final: 0.6978 (tmm) REVERT: A 590 MET cc_start: 0.5879 (mmm) cc_final: 0.4711 (mmm) REVERT: A 595 GLN cc_start: 0.8285 (mt0) cc_final: 0.7853 (mt0) REVERT: A 605 PHE cc_start: 0.8424 (m-80) cc_final: 0.8072 (m-80) REVERT: A 625 TYR cc_start: 0.4314 (t80) cc_final: 0.4005 (t80) REVERT: A 771 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.6903 (ttt) REVERT: A 989 LEU cc_start: 0.6937 (mp) cc_final: 0.6693 (mp) REVERT: A 1049 MET cc_start: 0.8115 (tmm) cc_final: 0.7831 (tmm) REVERT: A 1059 LYS cc_start: 0.7485 (tttp) cc_final: 0.7071 (mptt) REVERT: A 1067 CYS cc_start: 0.8107 (m) cc_final: 0.7872 (m) REVERT: A 1110 SER cc_start: 0.8620 (t) cc_final: 0.8392 (m) REVERT: A 1120 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7995 (ttm110) REVERT: A 1163 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8362 (t) REVERT: A 1165 GLU cc_start: 0.8626 (tt0) cc_final: 0.7986 (mm-30) REVERT: A 1201 MET cc_start: 0.8062 (tpp) cc_final: 0.7608 (tpp) REVERT: A 1240 MET cc_start: 0.9055 (mmp) cc_final: 0.8691 (tpp) REVERT: A 1281 MET cc_start: 0.7942 (mpp) cc_final: 0.7545 (mpp) REVERT: A 1292 MET cc_start: 0.6273 (mmp) cc_final: 0.5251 (mtt) REVERT: A 1325 ASP cc_start: 0.8417 (m-30) cc_final: 0.8126 (t0) REVERT: A 1329 MET cc_start: 0.8139 (mmt) cc_final: 0.7661 (ppp) REVERT: A 1336 MET cc_start: 0.8590 (ttt) cc_final: 0.8253 (tmm) REVERT: A 1372 LYS cc_start: 0.9039 (mmtp) cc_final: 0.8725 (mtmt) REVERT: A 1446 MET cc_start: 0.8051 (ttt) cc_final: 0.7848 (ttm) REVERT: A 1475 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6298 (p90) REVERT: A 1515 LEU cc_start: 0.8751 (mt) cc_final: 0.8456 (mt) REVERT: B 28 VAL cc_start: 0.9175 (p) cc_final: 0.8965 (p) REVERT: B 62 TRP cc_start: 0.8473 (m100) cc_final: 0.7639 (m-10) REVERT: B 125 TYR cc_start: 0.8022 (t80) cc_final: 0.6818 (t80) REVERT: B 163 GLU cc_start: 0.8457 (tt0) cc_final: 0.7895 (tm-30) REVERT: B 165 MET cc_start: 0.8044 (mmm) cc_final: 0.7426 (tmm) REVERT: B 167 TYR cc_start: 0.8066 (m-80) cc_final: 0.7338 (m-80) REVERT: B 177 LEU cc_start: 0.8612 (mt) cc_final: 0.8366 (mt) outliers start: 75 outliers final: 52 residues processed: 343 average time/residue: 0.1903 time to fit residues: 96.2502 Evaluate side-chains 344 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1120 ARG Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10874 Z= 0.268 Angle : 0.720 10.127 14745 Z= 0.373 Chirality : 0.044 0.202 1751 Planarity : 0.005 0.092 1789 Dihedral : 7.714 85.160 1757 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.64 % Favored : 92.90 % Rotamer: Outliers : 6.19 % Allowed : 25.22 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1296 helix: 0.16 (0.17), residues: 851 sheet: -0.84 (0.67), residues: 52 loop : -2.42 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.007 0.002 HIS A 588 PHE 0.024 0.002 PHE A1499 TYR 0.016 0.002 TYR A1550 ARG 0.010 0.001 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 294 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6478 (mtt90) cc_final: 0.4940 (ptt180) REVERT: A 129 MET cc_start: 0.7911 (ttm) cc_final: 0.7413 (tmm) REVERT: A 166 LYS cc_start: 0.8863 (mttt) cc_final: 0.8648 (mmmt) REVERT: A 250 PHE cc_start: 0.7884 (t80) cc_final: 0.7044 (m-10) REVERT: A 305 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8303 (p90) REVERT: A 343 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7957 (p0) REVERT: A 391 PHE cc_start: 0.8485 (t80) cc_final: 0.8230 (t80) REVERT: A 393 LEU cc_start: 0.8312 (mt) cc_final: 0.8010 (tp) REVERT: A 563 MET cc_start: 0.6843 (tmm) cc_final: 0.6600 (tmm) REVERT: A 625 TYR cc_start: 0.4346 (t80) cc_final: 0.4138 (t80) REVERT: A 771 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.6681 (ttt) REVERT: A 989 LEU cc_start: 0.6955 (mp) cc_final: 0.6699 (mp) REVERT: A 993 CYS cc_start: 0.8797 (m) cc_final: 0.8527 (m) REVERT: A 1049 MET cc_start: 0.8166 (tmm) cc_final: 0.7824 (tmm) REVERT: A 1059 LYS cc_start: 0.7438 (tttp) cc_final: 0.7061 (mptt) REVERT: A 1061 TYR cc_start: 0.7889 (t80) cc_final: 0.7149 (t80) REVERT: A 1067 CYS cc_start: 0.8450 (m) cc_final: 0.7969 (m) REVERT: A 1110 SER cc_start: 0.8722 (t) cc_final: 0.8456 (m) REVERT: A 1163 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8423 (t) REVERT: A 1165 GLU cc_start: 0.8734 (tt0) cc_final: 0.7987 (mm-30) REVERT: A 1201 MET cc_start: 0.8119 (tpp) cc_final: 0.7533 (tpp) REVERT: A 1217 ASP cc_start: 0.8689 (t0) cc_final: 0.8467 (t0) REVERT: A 1240 MET cc_start: 0.9139 (mmp) cc_final: 0.8848 (tpp) REVERT: A 1281 MET cc_start: 0.8009 (mpp) cc_final: 0.7594 (mpp) REVERT: A 1292 MET cc_start: 0.6483 (mmp) cc_final: 0.5522 (mtt) REVERT: A 1325 ASP cc_start: 0.8426 (m-30) cc_final: 0.8202 (t0) REVERT: A 1329 MET cc_start: 0.8328 (mmt) cc_final: 0.7839 (ppp) REVERT: A 1336 MET cc_start: 0.8700 (ttt) cc_final: 0.8268 (tmm) REVERT: A 1372 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8715 (mtmt) REVERT: A 1456 LEU cc_start: 0.8883 (tp) cc_final: 0.8518 (tp) REVERT: A 1475 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6373 (p90) REVERT: B 28 VAL cc_start: 0.9238 (p) cc_final: 0.9037 (p) REVERT: B 62 TRP cc_start: 0.8465 (m100) cc_final: 0.7670 (m-10) REVERT: B 96 MET cc_start: 0.7898 (ttm) cc_final: 0.7599 (ttm) REVERT: B 148 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8473 (p0) REVERT: B 163 GLU cc_start: 0.8478 (tt0) cc_final: 0.7930 (tm-30) REVERT: B 165 MET cc_start: 0.8070 (mmm) cc_final: 0.7449 (tmm) REVERT: B 167 TYR cc_start: 0.8132 (m-80) cc_final: 0.7522 (m-80) REVERT: B 177 LEU cc_start: 0.8541 (mt) cc_final: 0.8258 (mt) outliers start: 69 outliers final: 45 residues processed: 336 average time/residue: 0.1836 time to fit residues: 91.7677 Evaluate side-chains 335 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 GLN A1335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10874 Z= 0.193 Angle : 0.698 11.694 14745 Z= 0.355 Chirality : 0.043 0.216 1751 Planarity : 0.004 0.096 1789 Dihedral : 7.138 82.729 1751 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.86 % Favored : 93.52 % Rotamer: Outliers : 5.03 % Allowed : 27.47 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1296 helix: 0.36 (0.18), residues: 846 sheet: -0.62 (0.72), residues: 49 loop : -2.21 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.004 0.001 HIS A 588 PHE 0.028 0.001 PHE A1499 TYR 0.018 0.001 TYR B 125 ARG 0.007 0.000 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 297 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6453 (mtt90) cc_final: 0.4921 (ptt180) REVERT: A 129 MET cc_start: 0.7916 (ttm) cc_final: 0.7384 (tmm) REVERT: A 250 PHE cc_start: 0.7881 (t80) cc_final: 0.6952 (m-10) REVERT: A 266 ASN cc_start: 0.8987 (m-40) cc_final: 0.8210 (m-40) REVERT: A 343 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7870 (p0) REVERT: A 344 TYR cc_start: 0.8750 (m-80) cc_final: 0.8323 (m-80) REVERT: A 391 PHE cc_start: 0.8448 (t80) cc_final: 0.8243 (t80) REVERT: A 393 LEU cc_start: 0.8057 (mt) cc_final: 0.7797 (tp) REVERT: A 563 MET cc_start: 0.6855 (tmm) cc_final: 0.6606 (tmm) REVERT: A 605 PHE cc_start: 0.8489 (m-80) cc_final: 0.8183 (m-10) REVERT: A 612 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 625 TYR cc_start: 0.4583 (t80) cc_final: 0.4134 (t80) REVERT: A 771 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.6829 (ttt) REVERT: A 993 CYS cc_start: 0.8811 (m) cc_final: 0.8487 (m) REVERT: A 1049 MET cc_start: 0.8045 (tmm) cc_final: 0.7607 (tmm) REVERT: A 1059 LYS cc_start: 0.7500 (tttp) cc_final: 0.7101 (mptt) REVERT: A 1061 TYR cc_start: 0.7806 (t80) cc_final: 0.7088 (t80) REVERT: A 1067 CYS cc_start: 0.8464 (m) cc_final: 0.7988 (m) REVERT: A 1110 SER cc_start: 0.8598 (t) cc_final: 0.8380 (m) REVERT: A 1144 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 1163 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8427 (t) REVERT: A 1165 GLU cc_start: 0.8636 (tt0) cc_final: 0.7948 (mm-30) REVERT: A 1201 MET cc_start: 0.8021 (tpp) cc_final: 0.7410 (tpp) REVERT: A 1240 MET cc_start: 0.9180 (mmp) cc_final: 0.8921 (tpp) REVERT: A 1281 MET cc_start: 0.7905 (mpp) cc_final: 0.7502 (mpp) REVERT: A 1292 MET cc_start: 0.6495 (mmp) cc_final: 0.5473 (mtt) REVERT: A 1325 ASP cc_start: 0.8433 (m-30) cc_final: 0.8137 (t0) REVERT: A 1329 MET cc_start: 0.8309 (mmt) cc_final: 0.7838 (ppp) REVERT: A 1372 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8747 (mtmt) REVERT: A 1438 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6356 (tmt170) REVERT: A 1475 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6311 (p90) REVERT: A 1515 LEU cc_start: 0.8801 (mt) cc_final: 0.8503 (mt) REVERT: A 1548 CYS cc_start: 0.8211 (m) cc_final: 0.7384 (m) REVERT: B 62 TRP cc_start: 0.8488 (m100) cc_final: 0.7647 (m-10) REVERT: B 96 MET cc_start: 0.7750 (ttm) cc_final: 0.7430 (ttm) REVERT: B 125 TYR cc_start: 0.7977 (t80) cc_final: 0.6828 (t80) REVERT: B 148 ASN cc_start: 0.8700 (t0) cc_final: 0.8469 (p0) REVERT: B 163 GLU cc_start: 0.8457 (tt0) cc_final: 0.7819 (tm-30) REVERT: B 165 MET cc_start: 0.8070 (mmm) cc_final: 0.7429 (tmm) REVERT: B 167 TYR cc_start: 0.8156 (m-80) cc_final: 0.7465 (m-80) REVERT: B 177 LEU cc_start: 0.8576 (mt) cc_final: 0.8319 (mt) outliers start: 56 outliers final: 43 residues processed: 332 average time/residue: 0.1954 time to fit residues: 95.9227 Evaluate side-chains 342 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1231 GLN Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10874 Z= 0.203 Angle : 0.696 9.844 14745 Z= 0.357 Chirality : 0.042 0.199 1751 Planarity : 0.004 0.090 1789 Dihedral : 6.944 82.596 1751 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.94 % Favored : 93.52 % Rotamer: Outliers : 5.30 % Allowed : 27.02 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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 (0.23), residues: 1296 helix: 0.48 (0.18), residues: 848 sheet: -0.55 (0.71), residues: 49 loop : -2.16 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.004 0.001 HIS A 588 PHE 0.031 0.001 PHE A1499 TYR 0.015 0.001 TYR B 125 ARG 0.007 0.001 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 291 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6463 (mtt90) cc_final: 0.4913 (ptt180) REVERT: A 129 MET cc_start: 0.7912 (ttm) cc_final: 0.7482 (tmm) REVERT: A 250 PHE cc_start: 0.7847 (t80) cc_final: 0.6965 (m-10) REVERT: A 266 ASN cc_start: 0.8985 (m-40) cc_final: 0.8218 (m-40) REVERT: A 343 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 344 TYR cc_start: 0.8765 (m-80) cc_final: 0.8340 (m-80) REVERT: A 563 MET cc_start: 0.6816 (tmm) cc_final: 0.6605 (tmm) REVERT: A 612 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: A 625 TYR cc_start: 0.4466 (t80) cc_final: 0.4048 (t80) REVERT: A 771 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.6849 (ttt) REVERT: A 993 CYS cc_start: 0.8740 (m) cc_final: 0.8500 (m) REVERT: A 1009 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7961 (mmp) REVERT: A 1059 LYS cc_start: 0.7510 (tttp) cc_final: 0.7111 (mptt) REVERT: A 1061 TYR cc_start: 0.7812 (t80) cc_final: 0.7041 (t80) REVERT: A 1067 CYS cc_start: 0.8386 (m) cc_final: 0.7812 (m) REVERT: A 1110 SER cc_start: 0.8614 (t) cc_final: 0.8374 (m) REVERT: A 1144 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 1163 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8438 (t) REVERT: A 1165 GLU cc_start: 0.8617 (tt0) cc_final: 0.7969 (mm-30) REVERT: A 1201 MET cc_start: 0.7955 (tpp) cc_final: 0.7296 (tpp) REVERT: A 1240 MET cc_start: 0.9164 (mmp) cc_final: 0.8914 (tpp) REVERT: A 1281 MET cc_start: 0.7839 (mpp) cc_final: 0.7393 (mpp) REVERT: A 1292 MET cc_start: 0.6524 (mmp) cc_final: 0.5489 (mtt) REVERT: A 1325 ASP cc_start: 0.8415 (m-30) cc_final: 0.8124 (t0) REVERT: A 1329 MET cc_start: 0.8288 (mmt) cc_final: 0.7754 (ppp) REVERT: A 1372 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8745 (mtmt) REVERT: A 1438 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6360 (tmt170) REVERT: A 1475 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6387 (p90) REVERT: A 1515 LEU cc_start: 0.8808 (mt) cc_final: 0.8502 (mt) REVERT: B 62 TRP cc_start: 0.8472 (m100) cc_final: 0.7624 (m-10) REVERT: B 96 MET cc_start: 0.7636 (ttm) cc_final: 0.7327 (ttm) REVERT: B 125 TYR cc_start: 0.8000 (t80) cc_final: 0.6812 (t80) REVERT: B 128 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7345 (mtm180) REVERT: B 148 ASN cc_start: 0.8709 (t0) cc_final: 0.8492 (p0) REVERT: B 163 GLU cc_start: 0.8440 (tt0) cc_final: 0.7959 (tm-30) REVERT: B 165 MET cc_start: 0.8038 (mmm) cc_final: 0.7386 (tmm) REVERT: B 167 TYR cc_start: 0.8050 (m-80) cc_final: 0.7485 (m-80) REVERT: B 177 LEU cc_start: 0.8512 (mt) cc_final: 0.8295 (mt) outliers start: 59 outliers final: 42 residues processed: 329 average time/residue: 0.1950 time to fit residues: 95.2044 Evaluate side-chains 331 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10874 Z= 0.269 Angle : 0.738 10.790 14745 Z= 0.379 Chirality : 0.044 0.257 1751 Planarity : 0.005 0.092 1789 Dihedral : 7.027 78.948 1751 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.25 % Favored : 93.21 % Rotamer: Outliers : 5.21 % Allowed : 27.29 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.24 % 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: -0.53 (0.23), residues: 1296 helix: 0.53 (0.18), residues: 854 sheet: -0.46 (0.69), residues: 51 loop : -2.26 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.006 0.001 HIS A 588 PHE 0.034 0.002 PHE A1499 TYR 0.016 0.001 TYR A1550 ARG 0.006 0.001 ARG A1111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 290 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6575 (mtt90) cc_final: 0.4909 (ptt180) REVERT: A 129 MET cc_start: 0.7939 (ttm) cc_final: 0.7497 (tmm) REVERT: A 250 PHE cc_start: 0.7915 (t80) cc_final: 0.7043 (m-10) REVERT: A 266 ASN cc_start: 0.9044 (m-40) cc_final: 0.8217 (m-40) REVERT: A 343 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8025 (p0) REVERT: A 369 MET cc_start: 0.9128 (mtp) cc_final: 0.8833 (mtm) REVERT: A 612 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: A 625 TYR cc_start: 0.4571 (t80) cc_final: 0.4255 (t80) REVERT: A 734 ASP cc_start: 0.8544 (t70) cc_final: 0.8265 (t0) REVERT: A 771 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6865 (ttt) REVERT: A 993 CYS cc_start: 0.8791 (m) cc_final: 0.8578 (m) REVERT: A 1059 LYS cc_start: 0.7568 (tttp) cc_final: 0.7128 (mptt) REVERT: A 1061 TYR cc_start: 0.7766 (t80) cc_final: 0.7098 (t80) REVERT: A 1067 CYS cc_start: 0.8552 (m) cc_final: 0.8007 (m) REVERT: A 1110 SER cc_start: 0.8649 (t) cc_final: 0.8409 (m) REVERT: A 1163 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8582 (t) REVERT: A 1165 GLU cc_start: 0.8520 (tt0) cc_final: 0.7927 (mm-30) REVERT: A 1240 MET cc_start: 0.9287 (mmp) cc_final: 0.9058 (tpp) REVERT: A 1281 MET cc_start: 0.7938 (mpp) cc_final: 0.7477 (mpp) REVERT: A 1292 MET cc_start: 0.6573 (mmp) cc_final: 0.5527 (mtt) REVERT: A 1325 ASP cc_start: 0.8427 (m-30) cc_final: 0.8174 (t0) REVERT: A 1329 MET cc_start: 0.8309 (mmt) cc_final: 0.7771 (ppp) REVERT: A 1336 MET cc_start: 0.8591 (ttt) cc_final: 0.8110 (tmm) REVERT: A 1372 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8733 (mtmt) REVERT: A 1445 MET cc_start: 0.8779 (tpp) cc_final: 0.8367 (ttp) REVERT: A 1456 LEU cc_start: 0.8868 (tp) cc_final: 0.8475 (tp) REVERT: A 1475 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6513 (p90) REVERT: A 1515 LEU cc_start: 0.8861 (mt) cc_final: 0.8575 (mt) REVERT: A 1548 CYS cc_start: 0.8205 (m) cc_final: 0.7516 (m) REVERT: B 62 TRP cc_start: 0.8424 (m100) cc_final: 0.7608 (m-10) REVERT: B 96 MET cc_start: 0.7940 (ttm) cc_final: 0.7559 (ttm) REVERT: B 125 TYR cc_start: 0.8040 (t80) cc_final: 0.6758 (t80) REVERT: B 128 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7355 (mtm180) REVERT: B 148 ASN cc_start: 0.8738 (t0) cc_final: 0.8519 (p0) REVERT: B 163 GLU cc_start: 0.8496 (tt0) cc_final: 0.7868 (tm-30) REVERT: B 165 MET cc_start: 0.8062 (mmm) cc_final: 0.7371 (tmm) REVERT: B 167 TYR cc_start: 0.8187 (m-80) cc_final: 0.7516 (m-80) REVERT: B 177 LEU cc_start: 0.8492 (mt) cc_final: 0.8168 (mt) outliers start: 58 outliers final: 42 residues processed: 324 average time/residue: 0.1887 time to fit residues: 91.3323 Evaluate side-chains 328 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 281 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 173 CYS Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ASN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1163 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113119 restraints weight = 22348.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115858 restraints weight = 11884.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117598 restraints weight = 7773.633| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10874 Z= 0.208 Angle : 0.704 9.697 14745 Z= 0.360 Chirality : 0.043 0.248 1751 Planarity : 0.004 0.091 1789 Dihedral : 6.884 79.065 1751 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.02 % Favored : 93.44 % Rotamer: Outliers : 4.49 % Allowed : 28.28 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.16 % 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: -0.28 (0.23), residues: 1296 helix: 0.70 (0.18), residues: 840 sheet: -0.50 (0.70), residues: 49 loop : -1.97 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.006 0.001 HIS A 731 PHE 0.026 0.001 PHE A1499 TYR 0.018 0.001 TYR B 125 ARG 0.006 0.001 ARG A1111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.82 seconds wall clock time: 50 minutes 44.67 seconds (3044.67 seconds total)