Starting phenix.real_space_refine on Thu Feb 15 00:28:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/02_2024/5xsy_6770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/02_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_6770/02_2024/5xsy_6770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/02_2024/5xsy_6770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/02_2024/5xsy_6770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xsy_6770/02_2024/5xsy_6770.pdb" } 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 Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1028": "NH1" <-> "NH2" Residue "A ARG 1060": "NH1" <-> "NH2" Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A ARG 1157": "NH1" <-> "NH2" Residue "A ARG 1188": "NH1" <-> "NH2" Residue "A ARG 1226": "NH1" <-> "NH2" Residue "A ARG 1377": "NH1" <-> "NH2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A ARG 1429": "NH1" <-> "NH2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ASP 1521": "OD1" <-> "OD2" Residue "A GLU 1527": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.90, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.36 Conformation dependent library (CDL) restraints added in 1.8 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: 1.19 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: 2.99 Time building geometry restraints manager: 4.68 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: 81.30 - 93.36: 5 93.36 - 105.41: 201 105.41 - 117.47: 7772 117.47 - 129.53: 6689 129.53 - 141.59: 78 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 2.440 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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.270 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 30.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- 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 : 1.181 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: 0.2280 time to fit residues: 150.9895 Evaluate side-chains 350 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 310 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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: 0.7980 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 125 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN A 365 ASN A 409 ASN A 560 HIS A 628 GLN A 631 ASN A 690 ASN ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 GLN A1312 GLN B 73 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10874 Z= 0.268 Angle : 0.844 11.639 14745 Z= 0.442 Chirality : 0.047 0.255 1751 Planarity : 0.006 0.088 1789 Dihedral : 15.484 86.016 1824 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.02 % Favored : 93.36 % Rotamer: Outliers : 6.73 % Allowed : 17.59 % Favored : 75.67 % 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: -2.70 (0.21), residues: 1296 helix: -1.20 (0.16), residues: 832 sheet: -2.46 (0.58), residues: 66 loop : -2.68 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1215 HIS 0.008 0.002 HIS A 588 PHE 0.024 0.002 PHE A 177 TYR 0.024 0.002 TYR B 110 ARG 0.006 0.001 ARG A1157 *********************** 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: 75 poor density : 362 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6668 (mtt90) cc_final: 0.5163 (ptt180) REVERT: A 129 MET cc_start: 0.7898 (ttm) cc_final: 0.7336 (tmm) REVERT: A 139 MET cc_start: 0.8733 (tpp) cc_final: 0.8159 (mtt) REVERT: A 232 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6448 (tpt90) REVERT: A 240 GLN cc_start: 0.7495 (tp40) cc_final: 0.7106 (tm-30) REVERT: A 250 PHE cc_start: 0.7794 (t80) cc_final: 0.6876 (m-10) REVERT: A 266 ASN cc_start: 0.8982 (m-40) cc_final: 0.8094 (m110) REVERT: A 300 GLU cc_start: 0.9216 (tt0) cc_final: 0.8971 (tt0) REVERT: A 365 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 382 PHE cc_start: 0.8796 (m-10) cc_final: 0.8582 (m-80) REVERT: A 384 MET cc_start: 0.8066 (mmp) cc_final: 0.7857 (mmm) REVERT: A 407 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7464 (tt0) REVERT: A 595 GLN cc_start: 0.8315 (mt0) cc_final: 0.8053 (mt0) REVERT: A 625 TYR cc_start: 0.5254 (t80) cc_final: 0.4888 (t80) REVERT: A 634 ASP cc_start: 0.8690 (m-30) cc_final: 0.7496 (m-30) REVERT: A 660 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7740 (ttp-110) REVERT: A 690 ASN cc_start: 0.8962 (t0) cc_final: 0.8631 (t0) REVERT: A 726 GLU cc_start: 0.8340 (tt0) cc_final: 0.7875 (tm-30) REVERT: A 752 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8631 (mt-10) REVERT: A 771 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6770 (ttt) REVERT: A 1059 LYS cc_start: 0.7377 (tttp) cc_final: 0.7004 (mptt) REVERT: A 1061 TYR cc_start: 0.7991 (t80) cc_final: 0.7036 (t80) REVERT: A 1064 ASP cc_start: 0.7931 (m-30) cc_final: 0.7547 (t0) REVERT: A 1067 CYS cc_start: 0.8662 (m) cc_final: 0.8124 (m) REVERT: A 1110 SER cc_start: 0.8781 (t) cc_final: 0.8502 (m) REVERT: A 1120 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7911 (ttm110) REVERT: A 1165 GLU cc_start: 0.8672 (tt0) cc_final: 0.8057 (mm-30) REVERT: A 1192 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7934 (tm) REVERT: A 1203 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (t80) REVERT: A 1231 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 1240 MET cc_start: 0.8684 (mmp) cc_final: 0.8194 (tpp) REVERT: A 1266 ASN cc_start: 0.8313 (t0) cc_final: 0.8061 (t0) REVERT: A 1289 TYR cc_start: 0.8145 (t80) cc_final: 0.7790 (t80) REVERT: A 1294 LYS cc_start: 0.6960 (mttt) cc_final: 0.6743 (mmmt) REVERT: A 1325 ASP cc_start: 0.8501 (m-30) cc_final: 0.8173 (t0) REVERT: A 1326 ILE cc_start: 0.7978 (mt) cc_final: 0.7606 (mt) REVERT: A 1329 MET cc_start: 0.8262 (mmt) cc_final: 0.7869 (tmm) REVERT: A 1331 LEU cc_start: 0.8774 (mt) cc_final: 0.8497 (tp) REVERT: A 1377 ARG cc_start: 0.4271 (tpt170) cc_final: 0.3650 (mmt-90) REVERT: A 1446 MET cc_start: 0.8171 (ttt) cc_final: 0.7847 (ttm) REVERT: A 1468 PHE cc_start: 0.8434 (t80) cc_final: 0.8210 (t80) REVERT: B 27 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: B 28 VAL cc_start: 0.8886 (p) cc_final: 0.8636 (p) REVERT: B 62 TRP cc_start: 0.8159 (m100) cc_final: 0.7514 (m-10) REVERT: B 94 ASN cc_start: 0.8634 (t0) cc_final: 0.8332 (t0) REVERT: B 125 TYR cc_start: 0.7870 (t80) cc_final: 0.6799 (t80) REVERT: B 148 ASN cc_start: 0.8790 (t0) cc_final: 0.8253 (p0) REVERT: B 155 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8040 (mmt90) REVERT: B 163 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: B 165 MET cc_start: 0.8033 (mmm) cc_final: 0.7415 (tmm) REVERT: B 167 TYR cc_start: 0.8152 (m-80) cc_final: 0.7932 (m-80) REVERT: B 177 LEU cc_start: 0.8976 (mt) cc_final: 0.8749 (mt) outliers start: 75 outliers final: 33 residues processed: 404 average time/residue: 0.2381 time to fit residues: 139.0583 Evaluate side-chains 341 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 300 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 365 ASN 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 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 779 LEU 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 1192 LEU 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 1396 SER Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1497 CYS Chi-restraints excluded: chain A residue 1528 ASN 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 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: 0.5980 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 ASN A1528 ASN B 73 HIS B 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10874 Z= 0.251 Angle : 0.736 9.606 14745 Z= 0.384 Chirality : 0.045 0.250 1751 Planarity : 0.005 0.102 1789 Dihedral : 12.236 87.697 1786 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.71 % Favored : 92.75 % Rotamer: Outliers : 6.64 % Allowed : 22.26 % Favored : 71.10 % 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: -0.70 (0.17), residues: 840 sheet: -2.47 (0.55), residues: 66 loop : -2.57 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1507 HIS 0.011 0.003 HIS B 73 PHE 0.024 0.002 PHE A1486 TYR 0.016 0.002 TYR A 392 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 393 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 319 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6519 (mtt90) cc_final: 0.5096 (ptt-90) REVERT: A 129 MET cc_start: 0.7956 (ttm) cc_final: 0.7402 (tmm) REVERT: A 139 MET cc_start: 0.8762 (tpp) cc_final: 0.8245 (mtt) REVERT: A 232 ARG cc_start: 0.6759 (ttt180) cc_final: 0.6125 (tpt90) REVERT: A 240 GLN cc_start: 0.7488 (tp40) cc_final: 0.7255 (tm-30) REVERT: A 250 PHE cc_start: 0.7793 (t80) cc_final: 0.7005 (m-10) REVERT: A 264 MET cc_start: 0.9194 (ttm) cc_final: 0.8967 (tpp) REVERT: A 266 ASN cc_start: 0.9034 (m-40) cc_final: 0.8314 (m-40) REVERT: A 305 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8457 (p90) REVERT: A 326 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8612 (mp0) REVERT: A 369 MET cc_start: 0.8926 (mtm) cc_final: 0.8654 (mtm) REVERT: A 382 PHE cc_start: 0.8866 (m-10) cc_final: 0.8467 (m-80) REVERT: A 391 PHE cc_start: 0.8316 (t80) cc_final: 0.8064 (t80) REVERT: A 590 MET cc_start: 0.5962 (mmm) cc_final: 0.4939 (mmm) REVERT: A 595 GLN cc_start: 0.8263 (mt0) cc_final: 0.7882 (mt0) REVERT: A 726 GLU cc_start: 0.8261 (tt0) cc_final: 0.7890 (tm-30) REVERT: A 752 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8455 (mt-10) REVERT: A 771 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6614 (ttt) REVERT: A 1061 TYR cc_start: 0.7792 (t80) cc_final: 0.6989 (t80) REVERT: A 1064 ASP cc_start: 0.7521 (m-30) cc_final: 0.7209 (t0) REVERT: A 1067 CYS cc_start: 0.8538 (m) cc_final: 0.8063 (m) REVERT: A 1110 SER cc_start: 0.8602 (t) cc_final: 0.8295 (m) REVERT: A 1120 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8099 (ttm110) REVERT: A 1165 GLU cc_start: 0.8698 (tt0) cc_final: 0.8159 (mm-30) REVERT: A 1192 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 1194 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 1203 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8530 (t80) REVERT: A 1231 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 1266 ASN cc_start: 0.8491 (t0) cc_final: 0.8132 (t0) REVERT: A 1292 MET cc_start: 0.6051 (mmp) cc_final: 0.4888 (mtt) REVERT: A 1325 ASP cc_start: 0.8437 (m-30) cc_final: 0.8119 (t0) REVERT: A 1329 MET cc_start: 0.8279 (mmt) cc_final: 0.7855 (ppp) REVERT: A 1372 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8165 (mtmt) REVERT: A 1377 ARG cc_start: 0.3927 (tpt170) cc_final: 0.3276 (mmt-90) REVERT: A 1446 MET cc_start: 0.8197 (ttt) cc_final: 0.7982 (ttm) REVERT: A 1486 PHE cc_start: 0.8927 (m-80) cc_final: 0.8636 (m-10) REVERT: A 1508 ASP cc_start: 0.8929 (p0) cc_final: 0.8707 (p0) REVERT: B 28 VAL cc_start: 0.9024 (p) cc_final: 0.8812 (p) REVERT: B 49 MET cc_start: 0.8273 (ttp) cc_final: 0.7983 (ttp) REVERT: B 62 TRP cc_start: 0.8390 (m100) cc_final: 0.7525 (m-10) REVERT: B 70 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6426 (tp30) REVERT: B 94 ASN cc_start: 0.8680 (t0) cc_final: 0.8393 (t0) REVERT: B 96 MET cc_start: 0.7913 (ttm) cc_final: 0.7453 (ttm) REVERT: B 125 TYR cc_start: 0.7907 (t80) cc_final: 0.6820 (t80) REVERT: B 140 ASN cc_start: 0.8222 (p0) cc_final: 0.7850 (p0) REVERT: B 148 ASN cc_start: 0.8810 (t0) cc_final: 0.8365 (p0) REVERT: B 163 GLU cc_start: 0.8641 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 165 MET cc_start: 0.8036 (mmm) cc_final: 0.7463 (tmm) REVERT: B 167 TYR cc_start: 0.8059 (m-80) cc_final: 0.7585 (m-80) REVERT: B 173 LEU cc_start: 0.8674 (mt) cc_final: 0.8470 (mt) REVERT: B 174 GLN cc_start: 0.7915 (tp40) cc_final: 0.7590 (tp40) REVERT: B 177 LEU cc_start: 0.8753 (mt) cc_final: 0.8453 (mt) outliers start: 74 outliers final: 42 residues processed: 365 average time/residue: 0.2062 time to fit residues: 108.6518 Evaluate side-chains 331 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 647 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 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 1120 ARG Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1194 VAL 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 1380 PHE Chi-restraints excluded: chain A residue 1396 SER 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 1502 THR 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 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 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: 0.9980 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 343 ASN A 999 HIS A1231 GLN B 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10874 Z= 0.195 Angle : 0.695 11.073 14745 Z= 0.359 Chirality : 0.043 0.228 1751 Planarity : 0.005 0.113 1789 Dihedral : 10.103 89.074 1772 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.10 % Favored : 93.36 % Rotamer: Outliers : 5.92 % Allowed : 24.06 % 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: -1.68 (0.22), residues: 1296 helix: -0.33 (0.17), residues: 839 sheet: -1.94 (0.62), residues: 56 loop : -2.53 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1507 HIS 0.020 0.002 HIS B 73 PHE 0.020 0.001 PHE A1486 TYR 0.021 0.002 TYR A 625 ARG 0.007 0.000 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 379 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 313 time to evaluate : 1.158 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: 0.6495 (mtt90) cc_final: 0.5091 (ptt180) REVERT: A 129 MET cc_start: 0.7929 (ttm) cc_final: 0.7291 (tmm) REVERT: A 139 MET cc_start: 0.8765 (tpp) cc_final: 0.8251 (mtt) REVERT: A 250 PHE cc_start: 0.7783 (t80) cc_final: 0.6946 (m-10) REVERT: A 264 MET cc_start: 0.9174 (ttm) cc_final: 0.8920 (tpp) REVERT: A 266 ASN cc_start: 0.9042 (m-40) cc_final: 0.8231 (m-40) REVERT: A 369 MET cc_start: 0.9025 (mtm) cc_final: 0.8765 (mtm) REVERT: A 391 PHE cc_start: 0.8392 (t80) cc_final: 0.8151 (t80) REVERT: A 590 MET cc_start: 0.5856 (mmm) cc_final: 0.4854 (mmm) REVERT: A 595 GLN cc_start: 0.8311 (mt0) cc_final: 0.7960 (mt0) REVERT: A 726 GLU cc_start: 0.8326 (tt0) cc_final: 0.8042 (tm-30) REVERT: A 752 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8440 (mt-10) REVERT: A 771 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6625 (ttt) REVERT: A 1061 TYR cc_start: 0.7717 (t80) cc_final: 0.6775 (t80) REVERT: A 1067 CYS cc_start: 0.8343 (m) cc_final: 0.7940 (m) REVERT: A 1110 SER cc_start: 0.8594 (t) cc_final: 0.8296 (m) REVERT: A 1120 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (ttm110) REVERT: A 1163 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 1165 GLU cc_start: 0.8667 (tt0) cc_final: 0.8142 (mm-30) REVERT: A 1192 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8180 (tm) REVERT: A 1203 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8519 (t80) REVERT: A 1292 MET cc_start: 0.6085 (mmp) cc_final: 0.5020 (mtt) REVERT: A 1325 ASP cc_start: 0.8465 (m-30) cc_final: 0.8161 (t0) REVERT: A 1329 MET cc_start: 0.8235 (mmt) cc_final: 0.7804 (ppp) REVERT: A 1336 MET cc_start: 0.8743 (ttt) cc_final: 0.8471 (tpp) REVERT: A 1372 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8688 (mtmt) REVERT: A 1377 ARG cc_start: 0.3238 (tpt170) cc_final: 0.2548 (mmt-90) REVERT: A 1446 MET cc_start: 0.8473 (ttt) cc_final: 0.8224 (ttm) REVERT: A 1475 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.6586 (p90) REVERT: A 1508 ASP cc_start: 0.8918 (p0) cc_final: 0.8709 (p0) REVERT: A 1515 LEU cc_start: 0.8363 (mt) cc_final: 0.8057 (mt) REVERT: B 27 GLU cc_start: 0.8725 (pt0) cc_final: 0.8499 (pt0) REVERT: B 28 VAL cc_start: 0.9115 (p) cc_final: 0.8908 (p) REVERT: B 62 TRP cc_start: 0.8427 (m100) cc_final: 0.7573 (m-10) REVERT: B 70 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6536 (tp30) REVERT: B 94 ASN cc_start: 0.8699 (t0) cc_final: 0.8421 (t0) REVERT: B 96 MET cc_start: 0.8033 (ttm) cc_final: 0.7570 (ttm) REVERT: B 125 TYR cc_start: 0.7877 (t80) cc_final: 0.6803 (t80) REVERT: B 140 ASN cc_start: 0.8067 (p0) cc_final: 0.7745 (p0) REVERT: B 163 GLU cc_start: 0.8420 (tt0) cc_final: 0.7788 (tm-30) REVERT: B 165 MET cc_start: 0.8005 (mmm) cc_final: 0.7401 (tmm) REVERT: B 167 TYR cc_start: 0.8115 (m-80) cc_final: 0.7545 (m-80) REVERT: B 174 GLN cc_start: 0.7985 (tp40) cc_final: 0.7655 (tp40) REVERT: B 177 LEU cc_start: 0.8664 (mt) cc_final: 0.8408 (mt) outliers start: 66 outliers final: 44 residues processed: 356 average time/residue: 0.1920 time to fit residues: 99.9228 Evaluate side-chains 342 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 292 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 553 VAL 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 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 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 59 VAL 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 129 THR 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 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: 0.6980 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.0020 chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 overall best weight: 1.5490 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10874 Z= 0.229 Angle : 0.687 10.124 14745 Z= 0.354 Chirality : 0.043 0.265 1751 Planarity : 0.005 0.102 1789 Dihedral : 9.269 88.826 1769 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.71 % Favored : 92.75 % Rotamer: Outliers : 6.28 % Allowed : 25.13 % Favored : 68.58 % 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: -1.44 (0.22), residues: 1296 helix: -0.12 (0.17), residues: 842 sheet: -1.90 (0.58), residues: 61 loop : -2.49 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1507 HIS 0.006 0.001 HIS A 588 PHE 0.025 0.001 PHE A1486 TYR 0.028 0.001 TYR A 625 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 364 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6544 (mtt90) cc_final: 0.5106 (ptt180) REVERT: A 129 MET cc_start: 0.7976 (ttm) cc_final: 0.7320 (tmm) REVERT: A 133 PHE cc_start: 0.6818 (t80) cc_final: 0.6600 (t80) REVERT: A 139 MET cc_start: 0.8747 (tpp) cc_final: 0.8370 (mtt) REVERT: A 166 LYS cc_start: 0.8863 (mttt) cc_final: 0.8435 (mtmt) REVERT: A 241 MET cc_start: 0.7359 (tpp) cc_final: 0.7140 (mmt) REVERT: A 250 PHE cc_start: 0.7864 (t80) cc_final: 0.7015 (m-10) REVERT: A 266 ASN cc_start: 0.9078 (m-40) cc_final: 0.8248 (m-40) REVERT: A 305 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (p90) REVERT: A 343 ASN cc_start: 0.8057 (p0) cc_final: 0.7468 (p0) REVERT: A 369 MET cc_start: 0.9065 (mtm) cc_final: 0.8858 (mtp) REVERT: A 391 PHE cc_start: 0.8468 (t80) cc_final: 0.8222 (t80) REVERT: A 647 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.2343 (tt) REVERT: A 726 GLU cc_start: 0.8328 (tt0) cc_final: 0.8068 (tm-30) REVERT: A 752 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8410 (mt-10) REVERT: A 771 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6662 (ttt) REVERT: A 993 CYS cc_start: 0.8906 (m) cc_final: 0.8654 (m) REVERT: A 1061 TYR cc_start: 0.7828 (t80) cc_final: 0.7063 (t80) REVERT: A 1067 CYS cc_start: 0.8364 (m) cc_final: 0.8070 (m) REVERT: A 1110 SER cc_start: 0.8625 (t) cc_final: 0.8322 (m) REVERT: A 1120 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8001 (ttm110) REVERT: A 1163 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8707 (m) REVERT: A 1165 GLU cc_start: 0.8572 (tt0) cc_final: 0.8083 (mm-30) REVERT: A 1192 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8239 (tm) REVERT: A 1194 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8810 (m) REVERT: A 1203 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8551 (t80) REVERT: A 1281 MET cc_start: 0.8056 (mpp) cc_final: 0.7849 (mpp) REVERT: A 1292 MET cc_start: 0.6119 (mmp) cc_final: 0.5069 (mtt) REVERT: A 1325 ASP cc_start: 0.8453 (m-30) cc_final: 0.8164 (t0) REVERT: A 1329 MET cc_start: 0.8300 (mmt) cc_final: 0.7852 (ppp) REVERT: A 1372 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8710 (mtmt) REVERT: A 1377 ARG cc_start: 0.2858 (tpt170) cc_final: 0.2185 (mmt-90) REVERT: A 1446 MET cc_start: 0.8403 (ttt) cc_final: 0.8179 (ttm) REVERT: A 1456 LEU cc_start: 0.8886 (tp) cc_final: 0.8538 (tp) REVERT: A 1475 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.6600 (p90) REVERT: A 1485 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 1486 PHE cc_start: 0.8968 (m-80) cc_final: 0.8732 (m-10) REVERT: A 1515 LEU cc_start: 0.8537 (mt) cc_final: 0.8210 (mt) REVERT: B 62 TRP cc_start: 0.8380 (m100) cc_final: 0.7570 (m-10) REVERT: B 81 THR cc_start: 0.9192 (m) cc_final: 0.8827 (t) REVERT: B 94 ASN cc_start: 0.8747 (t0) cc_final: 0.8510 (t0) REVERT: B 96 MET cc_start: 0.8089 (ttm) cc_final: 0.7653 (ttm) REVERT: B 125 TYR cc_start: 0.7904 (t80) cc_final: 0.6845 (t80) REVERT: B 140 ASN cc_start: 0.8056 (p0) cc_final: 0.7793 (p0) REVERT: B 163 GLU cc_start: 0.8429 (tt0) cc_final: 0.7880 (tm-30) REVERT: B 165 MET cc_start: 0.8096 (mmm) cc_final: 0.7501 (tmm) REVERT: B 167 TYR cc_start: 0.8112 (m-80) cc_final: 0.7521 (m-80) REVERT: B 174 GLN cc_start: 0.7907 (tp40) cc_final: 0.7545 (tp40) REVERT: B 177 LEU cc_start: 0.8644 (mt) cc_final: 0.8396 (mt) outliers start: 70 outliers final: 50 residues processed: 343 average time/residue: 0.1915 time to fit residues: 97.5480 Evaluate side-chains 344 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 284 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 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 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 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 1194 VAL 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 1282 THR 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 1396 SER 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 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 73 HIS 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 162 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.0030 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10874 Z= 0.181 Angle : 0.684 14.861 14745 Z= 0.347 Chirality : 0.042 0.227 1751 Planarity : 0.004 0.097 1789 Dihedral : 8.535 87.425 1769 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.56 % Favored : 93.90 % Rotamer: Outliers : 5.75 % Allowed : 25.40 % Favored : 68.85 % 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: -1.16 (0.23), residues: 1296 helix: 0.09 (0.18), residues: 843 sheet: -1.62 (0.60), residues: 61 loop : -2.40 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1507 HIS 0.008 0.002 HIS B 73 PHE 0.021 0.001 PHE A1486 TYR 0.020 0.001 TYR A 625 ARG 0.009 0.000 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 364 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 300 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6533 (mtt90) cc_final: 0.5081 (ptt180) REVERT: A 129 MET cc_start: 0.8036 (ttm) cc_final: 0.7399 (tmm) REVERT: A 139 MET cc_start: 0.8729 (tpp) cc_final: 0.8363 (mtt) REVERT: A 166 LYS cc_start: 0.8924 (mttt) cc_final: 0.8628 (mmmm) REVERT: A 241 MET cc_start: 0.7278 (tpp) cc_final: 0.7054 (mmt) REVERT: A 250 PHE cc_start: 0.7831 (t80) cc_final: 0.6942 (m-10) REVERT: A 266 ASN cc_start: 0.9002 (m-40) cc_final: 0.8196 (m-40) REVERT: A 343 ASN cc_start: 0.8039 (p0) cc_final: 0.7422 (p0) REVERT: A 369 MET cc_start: 0.9145 (mtm) cc_final: 0.8912 (mtp) REVERT: A 391 PHE cc_start: 0.8463 (t80) cc_final: 0.8252 (t80) REVERT: A 563 MET cc_start: 0.6781 (tmm) cc_final: 0.6511 (tmm) REVERT: A 726 GLU cc_start: 0.8170 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 771 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6676 (ttt) REVERT: A 779 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7567 (tm) REVERT: A 993 CYS cc_start: 0.8840 (m) cc_final: 0.8538 (m) REVERT: A 1061 TYR cc_start: 0.7689 (t80) cc_final: 0.6899 (t80) REVERT: A 1067 CYS cc_start: 0.8363 (m) cc_final: 0.7891 (m) REVERT: A 1110 SER cc_start: 0.8515 (t) cc_final: 0.8184 (m) REVERT: A 1120 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8063 (ttm110) REVERT: A 1163 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8350 (t) REVERT: A 1165 GLU cc_start: 0.8531 (tt0) cc_final: 0.7894 (mm-30) REVERT: A 1192 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8150 (tm) REVERT: A 1194 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8661 (m) REVERT: A 1203 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8497 (t80) REVERT: A 1240 MET cc_start: 0.9125 (mmp) cc_final: 0.8754 (tpp) REVERT: A 1281 MET cc_start: 0.7954 (mpp) cc_final: 0.7642 (mpp) REVERT: A 1292 MET cc_start: 0.6266 (mmp) cc_final: 0.5259 (mtt) REVERT: A 1325 ASP cc_start: 0.8510 (m-30) cc_final: 0.8210 (t0) REVERT: A 1329 MET cc_start: 0.8290 (mmt) cc_final: 0.7825 (ppp) REVERT: A 1336 MET cc_start: 0.8514 (ttt) cc_final: 0.8207 (tpp) REVERT: A 1372 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8695 (mtmt) REVERT: A 1377 ARG cc_start: 0.2652 (tpt170) cc_final: 0.1976 (mmt-90) REVERT: A 1456 LEU cc_start: 0.8874 (tp) cc_final: 0.8494 (tp) REVERT: A 1475 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 1515 LEU cc_start: 0.8547 (mt) cc_final: 0.8188 (mt) REVERT: B 62 TRP cc_start: 0.8428 (m100) cc_final: 0.7784 (m-10) REVERT: B 94 ASN cc_start: 0.8768 (t0) cc_final: 0.8532 (t0) REVERT: B 96 MET cc_start: 0.8125 (ttm) cc_final: 0.7674 (ttm) REVERT: B 125 TYR cc_start: 0.7898 (t80) cc_final: 0.6834 (t80) REVERT: B 140 ASN cc_start: 0.8031 (p0) cc_final: 0.7817 (p0) REVERT: B 163 GLU cc_start: 0.8469 (tt0) cc_final: 0.7914 (tm-30) REVERT: B 165 MET cc_start: 0.8103 (mmm) cc_final: 0.7460 (tmm) REVERT: B 167 TYR cc_start: 0.8111 (m-80) cc_final: 0.7400 (m-80) REVERT: B 173 LEU cc_start: 0.8573 (mt) cc_final: 0.8322 (mt) REVERT: B 174 GLN cc_start: 0.7958 (tp40) cc_final: 0.7589 (tp40) REVERT: B 177 LEU cc_start: 0.8637 (mt) cc_final: 0.8407 (mt) outliers start: 64 outliers final: 41 residues processed: 341 average time/residue: 0.1935 time to fit residues: 97.4435 Evaluate side-chains 336 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 287 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 187 LEU 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 306 LEU 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 662 LEU Chi-restraints excluded: chain A residue 688 LEU 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 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 1194 VAL Chi-restraints excluded: chain A residue 1203 TYR 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 1441 LEU 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 30 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 HIS 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 148 ASN 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: 7.9990 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 79 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.7482 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10874 Z= 0.241 Angle : 0.725 17.300 14745 Z= 0.365 Chirality : 0.043 0.248 1751 Planarity : 0.005 0.096 1789 Dihedral : 8.000 86.923 1760 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.33 % Favored : 93.13 % Rotamer: Outliers : 6.37 % Allowed : 25.31 % Favored : 68.31 % 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: -0.93 (0.23), residues: 1296 helix: 0.24 (0.18), residues: 845 sheet: -0.86 (0.67), residues: 51 loop : -2.38 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1066 HIS 0.007 0.002 HIS A 588 PHE 0.029 0.002 PHE A1486 TYR 0.019 0.001 TYR A 625 ARG 0.006 0.001 ARG B 123 *********************** 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 365 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6539 (mtt90) cc_final: 0.5031 (ptt180) REVERT: A 129 MET cc_start: 0.8078 (ttm) cc_final: 0.7498 (tmm) REVERT: A 139 MET cc_start: 0.8750 (tpp) cc_final: 0.8376 (mtt) REVERT: A 166 LYS cc_start: 0.8872 (mttt) cc_final: 0.8550 (mmmm) REVERT: A 241 MET cc_start: 0.7292 (tpp) cc_final: 0.6876 (mmt) REVERT: A 250 PHE cc_start: 0.7902 (t80) cc_final: 0.7007 (m-10) REVERT: A 266 ASN cc_start: 0.9071 (m-40) cc_final: 0.8246 (m-40) REVERT: A 305 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8265 (p90) REVERT: A 343 ASN cc_start: 0.8268 (p0) cc_final: 0.7700 (p0) REVERT: A 369 MET cc_start: 0.9186 (mtm) cc_final: 0.8965 (mtp) REVERT: A 391 PHE cc_start: 0.8536 (t80) cc_final: 0.8286 (t80) REVERT: A 393 LEU cc_start: 0.8335 (mt) cc_final: 0.7905 (tp) REVERT: A 563 MET cc_start: 0.6756 (tmm) cc_final: 0.6491 (tmm) REVERT: A 771 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6718 (ttt) REVERT: A 779 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (tm) REVERT: A 993 CYS cc_start: 0.8743 (m) cc_final: 0.8473 (m) REVERT: A 1061 TYR cc_start: 0.7860 (t80) cc_final: 0.6998 (t80) REVERT: A 1067 CYS cc_start: 0.8380 (m) cc_final: 0.7970 (m) REVERT: A 1110 SER cc_start: 0.8649 (t) cc_final: 0.8345 (m) REVERT: A 1120 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8141 (ttm110) REVERT: A 1163 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8434 (t) REVERT: A 1165 GLU cc_start: 0.8649 (tt0) cc_final: 0.7968 (mm-30) REVERT: A 1173 ASN cc_start: 0.7373 (t0) cc_final: 0.7164 (t0) REVERT: A 1192 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8206 (tm) REVERT: A 1194 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8790 (m) REVERT: A 1203 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8555 (t80) REVERT: A 1240 MET cc_start: 0.9154 (mmp) cc_final: 0.8814 (tpp) REVERT: A 1281 MET cc_start: 0.7989 (mpp) cc_final: 0.7645 (mpp) REVERT: A 1292 MET cc_start: 0.6452 (mmp) cc_final: 0.5518 (mtt) REVERT: A 1325 ASP cc_start: 0.8549 (m-30) cc_final: 0.8251 (t0) REVERT: A 1329 MET cc_start: 0.8264 (mmt) cc_final: 0.7733 (ppp) REVERT: A 1336 MET cc_start: 0.8554 (ttt) cc_final: 0.8342 (ttt) REVERT: A 1372 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8708 (mtmt) REVERT: A 1377 ARG cc_start: 0.2561 (tpt170) cc_final: 0.1865 (mmt-90) REVERT: A 1456 LEU cc_start: 0.8884 (tp) cc_final: 0.8503 (tp) REVERT: A 1475 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.6436 (p90) REVERT: A 1515 LEU cc_start: 0.8801 (mt) cc_final: 0.8478 (mt) REVERT: B 94 ASN cc_start: 0.8792 (t0) cc_final: 0.8570 (t0) REVERT: B 96 MET cc_start: 0.8154 (ttm) cc_final: 0.7790 (ttm) REVERT: B 125 TYR cc_start: 0.7918 (t80) cc_final: 0.6913 (t80) REVERT: B 140 ASN cc_start: 0.8087 (p0) cc_final: 0.7849 (p0) REVERT: B 148 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8464 (p0) REVERT: B 163 GLU cc_start: 0.8479 (tt0) cc_final: 0.7932 (tm-30) REVERT: B 165 MET cc_start: 0.8046 (mmm) cc_final: 0.7376 (tmm) REVERT: B 167 TYR cc_start: 0.8215 (m-80) cc_final: 0.7629 (m-80) REVERT: B 174 GLN cc_start: 0.7971 (tp40) cc_final: 0.7602 (tp40) REVERT: B 177 LEU cc_start: 0.8650 (mt) cc_final: 0.8333 (mt) outliers start: 71 outliers final: 49 residues processed: 338 average time/residue: 0.1955 time to fit residues: 97.6590 Evaluate side-chains 347 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 195 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 ILE 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 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 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 1194 VAL 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 1282 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1380 PHE Chi-restraints excluded: chain A residue 1381 PHE Chi-restraints excluded: chain A residue 1396 SER 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 1472 ASN Chi-restraints excluded: chain A residue 1475 TYR Chi-restraints excluded: chain A residue 1498 LEU 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 148 ASN 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: 2.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 343 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5440 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= 0.205 Angle : 0.698 16.812 14745 Z= 0.350 Chirality : 0.043 0.256 1751 Planarity : 0.004 0.094 1789 Dihedral : 7.696 85.197 1760 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.63 % Favored : 93.90 % Rotamer: Outliers : 6.10 % Allowed : 26.21 % 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: -0.78 (0.23), residues: 1296 helix: 0.32 (0.18), residues: 854 sheet: -0.65 (0.69), residues: 51 loop : -2.31 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 PHE 0.019 0.001 PHE B 102 TYR 0.016 0.001 TYR A 625 ARG 0.007 0.000 ARG B 123 *********************** 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 365 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 297 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6467 (mtt90) cc_final: 0.4897 (ptt180) REVERT: A 129 MET cc_start: 0.8050 (ttm) cc_final: 0.7419 (tmm) REVERT: A 139 MET cc_start: 0.8745 (tpp) cc_final: 0.8376 (mtt) REVERT: A 166 LYS cc_start: 0.8869 (mttt) cc_final: 0.8567 (mmmm) REVERT: A 250 PHE cc_start: 0.7907 (t80) cc_final: 0.7009 (m-10) REVERT: A 266 ASN cc_start: 0.9052 (m-40) cc_final: 0.8239 (m-40) REVERT: A 305 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8172 (p90) REVERT: A 343 ASN cc_start: 0.8233 (p0) cc_final: 0.7647 (p0) REVERT: A 391 PHE cc_start: 0.8514 (t80) cc_final: 0.8295 (t80) REVERT: A 393 LEU cc_start: 0.8174 (mt) cc_final: 0.7792 (tp) REVERT: A 563 MET cc_start: 0.6736 (tmm) cc_final: 0.6486 (tmm) REVERT: A 749 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 771 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6694 (ttt) REVERT: A 779 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7993 (tm) REVERT: A 993 CYS cc_start: 0.8708 (m) cc_final: 0.8457 (m) REVERT: A 1061 TYR cc_start: 0.7832 (t80) cc_final: 0.6984 (t80) REVERT: A 1067 CYS cc_start: 0.8253 (m) cc_final: 0.7696 (m) REVERT: A 1120 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8000 (ttm110) REVERT: A 1163 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8174 (t) REVERT: A 1165 GLU cc_start: 0.8642 (tt0) cc_final: 0.7913 (mm-30) REVERT: A 1173 ASN cc_start: 0.7543 (t0) cc_final: 0.7337 (t0) REVERT: A 1192 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8128 (tm) REVERT: A 1194 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8722 (m) REVERT: A 1203 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8503 (t80) REVERT: A 1240 MET cc_start: 0.9126 (mmp) cc_final: 0.8801 (tpp) REVERT: A 1281 MET cc_start: 0.7958 (mpp) cc_final: 0.7622 (mpp) REVERT: A 1292 MET cc_start: 0.6465 (mmp) cc_final: 0.5527 (mtt) REVERT: A 1325 ASP cc_start: 0.8521 (m-30) cc_final: 0.8241 (t0) REVERT: A 1329 MET cc_start: 0.8244 (mmt) cc_final: 0.7712 (ppp) REVERT: A 1372 LYS cc_start: 0.9032 (mmtp) cc_final: 0.8720 (mtmt) REVERT: A 1456 LEU cc_start: 0.8872 (tp) cc_final: 0.8500 (tp) REVERT: A 1475 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.6540 (p90) REVERT: A 1515 LEU cc_start: 0.8790 (mt) cc_final: 0.8451 (mt) REVERT: A 1548 CYS cc_start: 0.8215 (m) cc_final: 0.7562 (m) REVERT: B 62 TRP cc_start: 0.8504 (m100) cc_final: 0.7753 (m-10) REVERT: B 85 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7670 (p0) REVERT: B 94 ASN cc_start: 0.8795 (t0) cc_final: 0.8568 (t0) REVERT: B 96 MET cc_start: 0.8182 (ttm) cc_final: 0.7855 (ttm) REVERT: B 125 TYR cc_start: 0.7921 (t80) cc_final: 0.6919 (t80) REVERT: B 148 ASN cc_start: 0.8685 (t0) cc_final: 0.8478 (p0) REVERT: B 163 GLU cc_start: 0.8465 (tt0) cc_final: 0.7921 (tm-30) REVERT: B 165 MET cc_start: 0.8054 (mmm) cc_final: 0.7367 (tmm) REVERT: B 167 TYR cc_start: 0.8055 (m-80) cc_final: 0.7456 (m-80) REVERT: B 174 GLN cc_start: 0.7958 (tp40) cc_final: 0.7582 (tp40) REVERT: B 177 LEU cc_start: 0.8617 (mt) cc_final: 0.8329 (mt) outliers start: 68 outliers final: 50 residues processed: 341 average time/residue: 0.1882 time to fit residues: 96.1934 Evaluate side-chains 349 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 289 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 195 THR 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 306 LEU 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 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 1051 LEU 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 1194 VAL Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1210 SER Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1282 THR 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 1437 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1472 ASN 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 28 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 85 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10874 Z= 0.208 Angle : 0.723 17.021 14745 Z= 0.358 Chirality : 0.043 0.267 1751 Planarity : 0.004 0.097 1789 Dihedral : 7.505 83.921 1760 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.56 % Favored : 92.98 % Rotamer: Outliers : 5.66 % Allowed : 27.47 % Favored : 66.88 % 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: -0.68 (0.23), residues: 1296 helix: 0.42 (0.18), residues: 850 sheet: -0.50 (0.70), residues: 49 loop : -2.31 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1507 HIS 0.005 0.001 HIS A 588 PHE 0.021 0.001 PHE A1468 TYR 0.015 0.001 TYR A 625 ARG 0.006 0.000 ARG B 123 *********************** 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 358 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 295 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6479 (mtt90) cc_final: 0.4886 (ptt180) REVERT: A 129 MET cc_start: 0.8021 (ttm) cc_final: 0.7418 (tmm) REVERT: A 139 MET cc_start: 0.8703 (tpp) cc_final: 0.8403 (mtt) REVERT: A 166 LYS cc_start: 0.8898 (mttt) cc_final: 0.8614 (mmmm) REVERT: A 250 PHE cc_start: 0.7965 (t80) cc_final: 0.7117 (m-10) REVERT: A 305 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8128 (p90) REVERT: A 343 ASN cc_start: 0.8225 (p0) cc_final: 0.7670 (p0) REVERT: A 344 TYR cc_start: 0.8768 (m-80) cc_final: 0.8227 (m-80) REVERT: A 357 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8960 (tp) REVERT: A 369 MET cc_start: 0.9023 (mtp) cc_final: 0.8775 (mtm) REVERT: A 393 LEU cc_start: 0.8130 (mt) cc_final: 0.7814 (tp) REVERT: A 563 MET cc_start: 0.6828 (tmm) cc_final: 0.6573 (tmm) REVERT: A 749 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 771 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6781 (ttt) REVERT: A 779 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7983 (tm) REVERT: A 993 CYS cc_start: 0.8676 (m) cc_final: 0.8428 (m) REVERT: A 1061 TYR cc_start: 0.7838 (t80) cc_final: 0.6978 (t80) REVERT: A 1067 CYS cc_start: 0.8224 (m) cc_final: 0.7637 (m) REVERT: A 1120 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (ttm110) REVERT: A 1144 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 1163 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8173 (t) REVERT: A 1165 GLU cc_start: 0.8593 (tt0) cc_final: 0.7884 (mm-30) REVERT: A 1173 ASN cc_start: 0.7548 (t0) cc_final: 0.7346 (t0) REVERT: A 1192 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8085 (tm) REVERT: A 1194 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8597 (m) REVERT: A 1203 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8475 (t80) REVERT: A 1217 ASP cc_start: 0.8548 (t0) cc_final: 0.8344 (t0) REVERT: A 1240 MET cc_start: 0.9081 (mmp) cc_final: 0.8760 (tpp) REVERT: A 1281 MET cc_start: 0.7901 (mpp) cc_final: 0.7533 (mpp) REVERT: A 1292 MET cc_start: 0.6496 (mmp) cc_final: 0.5547 (mtt) REVERT: A 1325 ASP cc_start: 0.8518 (m-30) cc_final: 0.8234 (t0) REVERT: A 1329 MET cc_start: 0.8230 (mmt) cc_final: 0.7707 (ppp) REVERT: A 1372 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8754 (mtmt) REVERT: A 1438 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6257 (tmt170) REVERT: A 1456 LEU cc_start: 0.8869 (tp) cc_final: 0.8490 (tp) REVERT: A 1475 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.6594 (p90) REVERT: A 1486 PHE cc_start: 0.8771 (m-10) cc_final: 0.8551 (m-10) REVERT: A 1515 LEU cc_start: 0.8820 (mt) cc_final: 0.8469 (mt) REVERT: A 1548 CYS cc_start: 0.8286 (m) cc_final: 0.7648 (m) REVERT: B 31 ASP cc_start: 0.8617 (m-30) cc_final: 0.8245 (m-30) REVERT: B 62 TRP cc_start: 0.8501 (m100) cc_final: 0.7752 (m-10) REVERT: B 94 ASN cc_start: 0.8790 (t0) cc_final: 0.8568 (t0) REVERT: B 96 MET cc_start: 0.8182 (ttm) cc_final: 0.7862 (ttm) REVERT: B 125 TYR cc_start: 0.8127 (t80) cc_final: 0.6708 (t80) REVERT: B 140 ASN cc_start: 0.8185 (p0) cc_final: 0.7368 (m-40) REVERT: B 163 GLU cc_start: 0.8456 (tt0) cc_final: 0.7910 (tm-30) REVERT: B 165 MET cc_start: 0.8058 (mmm) cc_final: 0.7363 (tmm) REVERT: B 167 TYR cc_start: 0.8047 (m-80) cc_final: 0.7418 (m-80) REVERT: B 174 GLN cc_start: 0.7957 (tp40) cc_final: 0.7582 (tp40) REVERT: B 177 LEU cc_start: 0.8606 (mt) cc_final: 0.8329 (mt) outliers start: 63 outliers final: 47 residues processed: 337 average time/residue: 0.1990 time to fit residues: 99.5442 Evaluate side-chains 346 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 195 THR 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 306 LEU Chi-restraints excluded: chain A residue 357 LEU 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 604 VAL 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 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 1051 LEU 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 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 1194 VAL 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 1282 THR 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 1437 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1472 ASN 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 B residue 28 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 75 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5723 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= 0.236 Angle : 0.733 17.710 14745 Z= 0.366 Chirality : 0.043 0.231 1751 Planarity : 0.004 0.094 1789 Dihedral : 7.488 82.860 1759 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.40 % Favored : 93.13 % Rotamer: Outliers : 5.83 % Allowed : 27.83 % Favored : 66.34 % 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: -0.56 (0.23), residues: 1296 helix: 0.52 (0.18), residues: 848 sheet: -0.71 (0.65), residues: 58 loop : -2.25 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.005 0.001 HIS A 588 PHE 0.025 0.002 PHE A 391 TYR 0.015 0.001 TYR A 625 ARG 0.005 0.001 ARG B 123 ********************** 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 350 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 285 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6530 (mtt90) cc_final: 0.4883 (ptt180) REVERT: A 129 MET cc_start: 0.7966 (ttm) cc_final: 0.7404 (tmm) REVERT: A 139 MET cc_start: 0.8711 (tpp) cc_final: 0.8400 (mtt) REVERT: A 166 LYS cc_start: 0.8838 (mttt) cc_final: 0.8375 (mtmt) REVERT: A 266 ASN cc_start: 0.9065 (m-40) cc_final: 0.8274 (m-40) REVERT: A 305 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8163 (p90) REVERT: A 343 ASN cc_start: 0.8276 (p0) cc_final: 0.7703 (p0) REVERT: A 344 TYR cc_start: 0.8780 (m-80) cc_final: 0.8257 (m-80) REVERT: A 357 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8877 (tp) REVERT: A 393 LEU cc_start: 0.8207 (mt) cc_final: 0.7869 (tp) REVERT: A 563 MET cc_start: 0.6813 (tmm) cc_final: 0.6559 (tmm) REVERT: A 582 PHE cc_start: 0.9158 (t80) cc_final: 0.8504 (t80) REVERT: A 590 MET cc_start: 0.4524 (mmp) cc_final: 0.4173 (mmp) REVERT: A 749 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 771 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6783 (ttt) REVERT: A 779 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7941 (tm) REVERT: A 993 CYS cc_start: 0.8732 (m) cc_final: 0.8472 (m) REVERT: A 1061 TYR cc_start: 0.8046 (t80) cc_final: 0.7340 (t80) REVERT: A 1120 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7942 (ttm110) REVERT: A 1163 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8115 (t) REVERT: A 1165 GLU cc_start: 0.8542 (tt0) cc_final: 0.7870 (mm-30) REVERT: A 1192 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8007 (tm) REVERT: A 1194 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8678 (m) REVERT: A 1203 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 1217 ASP cc_start: 0.8581 (t0) cc_final: 0.8375 (t0) REVERT: A 1240 MET cc_start: 0.9112 (mmp) cc_final: 0.8800 (tpp) REVERT: A 1281 MET cc_start: 0.7932 (mpp) cc_final: 0.7568 (mpp) REVERT: A 1292 MET cc_start: 0.6540 (mmp) cc_final: 0.5563 (mtt) REVERT: A 1325 ASP cc_start: 0.8510 (m-30) cc_final: 0.8239 (t0) REVERT: A 1329 MET cc_start: 0.8275 (mmt) cc_final: 0.7737 (ppp) REVERT: A 1372 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8709 (mtmt) REVERT: A 1475 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.6781 (p90) REVERT: A 1495 MET cc_start: 0.9184 (tpp) cc_final: 0.8884 (mmm) REVERT: A 1515 LEU cc_start: 0.8811 (mt) cc_final: 0.8465 (mt) REVERT: A 1548 CYS cc_start: 0.8311 (m) cc_final: 0.7675 (m) REVERT: B 62 TRP cc_start: 0.8512 (m100) cc_final: 0.7841 (m-10) REVERT: B 85 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7597 (p0) REVERT: B 94 ASN cc_start: 0.8796 (t0) cc_final: 0.8532 (t0) REVERT: B 96 MET cc_start: 0.8215 (ttm) cc_final: 0.7900 (ttm) REVERT: B 125 TYR cc_start: 0.7795 (t80) cc_final: 0.6696 (t80) REVERT: B 163 GLU cc_start: 0.8466 (tt0) cc_final: 0.7850 (tm-30) REVERT: B 165 MET cc_start: 0.8070 (mmm) cc_final: 0.7368 (tmm) REVERT: B 167 TYR cc_start: 0.8021 (m-80) cc_final: 0.7445 (m-80) REVERT: B 174 GLN cc_start: 0.7956 (tp40) cc_final: 0.7582 (tp40) REVERT: B 177 LEU cc_start: 0.8563 (mt) cc_final: 0.8263 (mt) outliers start: 65 outliers final: 48 residues processed: 327 average time/residue: 0.2044 time to fit residues: 100.2459 Evaluate side-chains 338 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 357 LEU 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 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 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 1051 LEU 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 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 1194 VAL 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 1282 THR Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 TYR 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 1437 ILE Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain A residue 1472 ASN 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 28 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 85 ASN 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: 0.3980 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 91 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 343 ASN A 579 ASN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114788 restraints weight = 21836.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117446 restraints weight = 11757.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119157 restraints weight = 7720.162| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10874 Z= 0.190 Angle : 0.731 17.600 14745 Z= 0.360 Chirality : 0.042 0.226 1751 Planarity : 0.004 0.092 1789 Dihedral : 7.249 82.936 1757 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.79 % Favored : 93.75 % Rotamer: Outliers : 4.76 % Allowed : 29.17 % Favored : 66.07 % 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: -0.41 (0.23), residues: 1296 helix: 0.65 (0.18), residues: 845 sheet: -0.65 (0.64), residues: 56 loop : -2.23 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1507 HIS 0.004 0.001 HIS A 731 PHE 0.027 0.001 PHE A1486 TYR 0.013 0.001 TYR A 625 ARG 0.006 0.001 ARG A 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.43 seconds wall clock time: 48 minutes 52.96 seconds (2932.96 seconds total)