Starting phenix.real_space_refine on Mon Oct 13 14:07:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soj_40659/10_2025/8soj_40659.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.042 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 97 5.16 5 C 10946 2.51 5 N 2988 2.21 5 O 3190 1.98 5 H 17267 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34490 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 18090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 18090 Classifications: {'peptide': 1158} Link IDs: {'PCIS': 6, 'PTRANS': 88, 'TRANS': 1063} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 6797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6797 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 17, 'TRANS': 410} Chain breaks: 1 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1897 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 7704 Classifications: {'peptide': 490} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 468} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15506 SG CYS A1043 77.163 92.425 71.542 1.00 77.69 S ATOM 15548 SG CYS A1046 74.525 95.132 70.928 1.00 94.18 S ATOM 15684 SG CYS A1055 78.159 95.560 69.743 1.00 99.30 S ATOM 15784 SG CYS A1062 77.492 95.679 73.394 1.00110.01 S ATOM 30547 SG CYS D 382 64.666 100.722 150.923 1.00103.05 S ATOM 30594 SG CYS D 385 64.810 104.124 149.472 1.00108.66 S ATOM 32449 SG CYS D 503 68.060 102.141 150.888 1.00116.52 S ATOM 32499 SG CYS D 506 65.517 103.834 153.110 1.00119.78 S Time building chain proxies: 6.05, per 1000 atoms: 0.18 Number of scatterers: 34490 At special positions: 0 Unit cell: (110.08, 140.18, 192.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 97 16.00 O 3190 8.00 N 2988 7.00 C 10946 6.00 H 17267 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1055 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1043 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1062 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1046 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 382 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 506 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 385 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 503 " Number of angles added : 12 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 26 sheets defined 29.5% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 37 through 53 removed outlier: 4.015A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.723A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.365A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 507 through 515 removed outlier: 3.907A pdb=" N LEU A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.825A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.541A pdb=" N LEU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 644 through 648 removed outlier: 3.531A pdb=" N LEU A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.534A pdb=" N SER A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.692A pdb=" N ARG A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 1011 through 1018 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 4.185A pdb=" N ALA A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1095 " --> pdb=" O HIS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1112 Processing helix chain 'A' and resid 1136 through 1146 Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'B' and resid 506 through 528 Processing helix chain 'B' and resid 563 through 580 Proline residue: B 574 - end of helix Processing helix chain 'B' and resid 603 through 622 Processing helix chain 'B' and resid 629 through 634 Processing helix chain 'B' and resid 635 through 643 Processing helix chain 'B' and resid 644 through 652 removed outlier: 3.558A pdb=" N HIS B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 657 through 680 Processing helix chain 'B' and resid 700 through 712 removed outlier: 3.530A pdb=" N ILE B 710 " --> pdb=" O LYS B 706 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 743 through 758 Processing helix chain 'C' and resid 11 through 17 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 212 through 217 removed outlier: 5.638A pdb=" N ASN D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 282 through 298 Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 373 through 376 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.605A pdb=" N LYS D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.558A pdb=" N GLN D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 removed outlier: 3.612A pdb=" N ILE D 634 " --> pdb=" O GLU D 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 631 through 634' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 4.687A pdb=" N LEU A 114 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N LEU A 179 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 143 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU A 181 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU A 145 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 4.687A pdb=" N LEU A 114 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 113 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 204 removed outlier: 5.905A pdb=" N ILE A 201 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 318 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 203 " --> pdb=" O LEU A 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.791A pdb=" N TRP A 299 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 301 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 298 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 7.180A pdb=" N ILE A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 233 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 248 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 352 Processing sheet with id=AA7, first strand: chain 'A' and resid 428 through 433 removed outlier: 3.528A pdb=" N ALA A 428 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A 400 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLY A 380 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 372 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 364 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 354 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N HIS A 407 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 356 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 596 removed outlier: 3.743A pdb=" N GLU A 662 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N SER A 629 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL A 690 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 692 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 633 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 592 through 596 removed outlier: 3.743A pdb=" N GLU A 662 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N SER A 629 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N VAL A 690 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE A 692 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 633 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 632 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 621 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 742 through 744 Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 781 removed outlier: 7.065A pdb=" N TYR A 764 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS A 738 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 766 " --> pdb=" O CYS A 736 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 732 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 772 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER A 730 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN A 774 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY A 728 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 816 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 991 through 996 removed outlier: 6.507A pdb=" N ARG A 966 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL A 982 " --> pdb=" O HIS A 945 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP A 947 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 929 " --> pdb=" O ILE A 950 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N CYS A 928 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 907 " --> pdb=" O CYS A 928 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 930 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG A 905 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 932 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 898 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 970 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 900 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS A 968 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 902 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 966 " --> pdb=" O ILE A 902 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 6.934A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1194 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A1041 " --> pdb=" O CYS A1050 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER A1048 " --> pdb=" O CYS A1043 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A1051 " --> pdb=" O LYS A1054 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1024 through 1027 removed outlier: 6.934A pdb=" N VAL A1156 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A1201 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A1158 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A1194 " --> pdb=" O GLU A1083 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG A1089 " --> pdb=" O CYS A1198 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N SER A1200 " --> pdb=" O ARG A1089 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A1036 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A1076 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1034 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLU A1078 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A1032 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1175 through 1181 Processing sheet with id=AB8, first strand: chain 'B' and resid 429 through 430 removed outlier: 6.248A pdb=" N ALA B 430 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU B 463 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 534 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER B 540 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA B 552 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 542 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE B 550 " --> pdb=" O ARG B 542 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 544 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG B 548 " --> pdb=" O TYR B 544 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ARG B 548 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN B 488 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP B 492 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR B 554 " --> pdb=" O TRP B 492 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B 471 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 477 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL B 469 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 479 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.685A pdb=" N LYS B 441 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 626 through 628 Processing sheet with id=AC2, first strand: chain 'B' and resid 725 through 726 removed outlier: 3.768A pdb=" N MET B 764 " --> pdb=" O TYR B 767 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B 769 " --> pdb=" O SER B 762 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER B 762 " --> pdb=" O THR B 769 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 44 through 45 removed outlier: 6.300A pdb=" N GLU C 78 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 91 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN C 80 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL C 89 " --> pdb=" O GLN C 80 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN C 82 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 87 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.660A pdb=" N SER D 260 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP D 219 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU D 265 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 221 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 178 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU D 173 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU D 180 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS D 171 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS D 182 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 274 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AC6, first strand: chain 'D' and resid 387 through 389 removed outlier: 3.557A pdb=" N ASP D 561 " --> pdb=" O PHE D 542 " (cutoff:3.500A) removed outlier: 12.632A pdb=" N VAL D 554 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N TYR D 622 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU D 556 " --> pdb=" O TYR D 622 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE D 624 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR D 558 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE D 606 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU D 366 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 549 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 368 " --> pdb=" O THR D 547 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 419 through 426 removed outlier: 3.660A pdb=" N ARG D 432 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 452 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU D 453 " --> pdb=" O ILE D 474 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 493 through 495 removed outlier: 3.579A pdb=" N LEU D 493 " --> pdb=" O HIS D 500 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 1890 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: 7.84 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17190 1.03 - 1.23: 331 1.23 - 1.43: 6973 1.43 - 1.63: 10261 1.63 - 1.82: 125 Bond restraints: 34880 Sorted by residual: bond pdb=" N LYS B 723 " pdb=" H LYS B 723 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N ARG B 410 " pdb=" H ARG B 410 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" CE LYS B 723 " pdb=" HE3 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" CE LYS B 723 " pdb=" HE2 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CB LYS B 723 " pdb=" HB2 LYS B 723 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 34875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 62917 2.48 - 4.96: 291 4.96 - 7.44: 10 7.44 - 9.92: 1 9.92 - 12.41: 2 Bond angle restraints: 63221 Sorted by residual: angle pdb=" CA THR C 43 " pdb=" C THR C 43 " pdb=" O THR C 43 " ideal model delta sigma weight residual 121.40 116.63 4.77 1.13e+00 7.83e-01 1.78e+01 angle pdb=" CA THR B 769 " pdb=" C THR B 769 " pdb=" O THR B 769 " ideal model delta sigma weight residual 120.89 116.27 4.62 1.10e+00 8.26e-01 1.76e+01 angle pdb=" CA LEU C 56 " pdb=" C LEU C 56 " pdb=" O LEU C 56 " ideal model delta sigma weight residual 121.19 116.64 4.55 1.10e+00 8.26e-01 1.71e+01 angle pdb=" CA LEU C 34 " pdb=" C LEU C 34 " pdb=" O LEU C 34 " ideal model delta sigma weight residual 120.56 116.82 3.74 9.70e-01 1.06e+00 1.48e+01 angle pdb=" CA MET C 45 " pdb=" C MET C 45 " pdb=" O MET C 45 " ideal model delta sigma weight residual 121.55 117.77 3.78 1.06e+00 8.90e-01 1.27e+01 ... (remaining 63216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 15123 16.80 - 33.59: 870 33.59 - 50.39: 312 50.39 - 67.19: 157 67.19 - 83.99: 21 Dihedral angle restraints: 16483 sinusoidal: 9081 harmonic: 7402 Sorted by residual: dihedral pdb=" CA GLU A 951 " pdb=" C GLU A 951 " pdb=" N ASP A 952 " pdb=" CA ASP A 952 " ideal model delta harmonic sigma weight residual 180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLN D 157 " pdb=" C GLN D 157 " pdb=" N PRO D 158 " pdb=" CA PRO D 158 " ideal model delta harmonic sigma weight residual 180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG D 328 " pdb=" C ARG D 328 " pdb=" N CYS D 329 " pdb=" CA CYS D 329 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2166 0.047 - 0.094: 414 0.094 - 0.142: 138 0.142 - 0.189: 10 0.189 - 0.236: 2 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA VAL C 42 " pdb=" N VAL C 42 " pdb=" C VAL C 42 " pdb=" CB VAL C 42 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL C 55 " pdb=" N VAL C 55 " pdb=" C VAL C 55 " pdb=" CB VAL C 55 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LEU C 34 " pdb=" N LEU C 34 " pdb=" C LEU C 34 " pdb=" CB LEU C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 2727 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 31 " -0.527 9.50e-02 1.11e+02 3.85e-01 2.67e+03 pdb=" NE ARG C 31 " -0.149 2.00e-02 2.50e+03 pdb=" CZ ARG C 31 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 31 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 31 " 0.036 2.00e-02 2.50e+03 pdb="HH11 ARG C 31 " 0.739 2.00e-02 2.50e+03 pdb="HH12 ARG C 31 " -0.689 2.00e-02 2.50e+03 pdb="HH21 ARG C 31 " 0.097 2.00e-02 2.50e+03 pdb="HH22 ARG C 31 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 54 " 0.242 2.00e-02 2.50e+03 2.87e-01 1.24e+03 pdb=" CD GLN C 54 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN C 54 " -0.225 2.00e-02 2.50e+03 pdb=" NE2 GLN C 54 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN C 54 " -0.432 2.00e-02 2.50e+03 pdb="HE22 GLN C 54 " 0.447 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 41 " -0.631 9.50e-02 1.11e+02 2.11e-01 4.95e+01 pdb=" NE ARG C 41 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG C 41 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 41 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 41 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG C 41 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 41 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG C 41 " -0.011 2.00e-02 2.50e+03 pdb="HH22 ARG C 41 " -0.000 2.00e-02 2.50e+03 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 255 1.96 - 2.62: 40371 2.62 - 3.28: 103688 3.28 - 3.94: 127248 3.94 - 4.60: 199661 Nonbonded interactions: 471223 Sorted by model distance: nonbonded pdb=" HG2 LYS B 723 " pdb=" HZ3 LYS B 723 " model vdw 1.297 2.270 nonbonded pdb=" OE2 GLU A 145 " pdb="HH22 ARG A 393 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASP A 137 " pdb=" HG1 THR A 139 " model vdw 1.635 2.450 nonbonded pdb=" OD2 ASP D 561 " pdb=" H PHE D 565 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP D 617 " pdb="HD21 ASN D 618 " model vdw 1.640 2.450 ... (remaining 471218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 38.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 : 0.003 0.041 17621 Z= 0.171 Angle : 0.650 11.272 23959 Z= 0.356 Chirality : 0.043 0.236 2730 Planarity : 0.007 0.281 3086 Dihedral : 12.259 83.987 6558 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.04 % Favored : 94.73 % Rotamer: Outliers : 0.52 % Allowed : 5.38 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.16), residues: 2181 helix: -1.46 (0.19), residues: 526 sheet: -1.15 (0.21), residues: 506 loop : -1.62 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 41 TYR 0.027 0.002 TYR B 767 PHE 0.015 0.001 PHE A1040 TRP 0.017 0.001 TRP C 13 HIS 0.005 0.001 HIS A1091 Details of bonding type rmsd covalent geometry : bond 0.00321 (17613) covalent geometry : angle 0.64176 (23947) hydrogen bonds : bond 0.16544 ( 674) hydrogen bonds : angle 7.84306 ( 1890) metal coordination : bond 0.00502 ( 8) metal coordination : angle 4.54316 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7912 (ptm) cc_final: 0.7681 (ptm) REVERT: A 892 THR cc_start: 0.7383 (m) cc_final: 0.7077 (m) REVERT: A 1078 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6215 (tm-30) REVERT: B 721 MET cc_start: 0.4031 (mpp) cc_final: 0.3549 (mmm) REVERT: D 327 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.5699 (tt0) REVERT: D 368 SER cc_start: 0.9051 (p) cc_final: 0.8660 (t) REVERT: D 575 MET cc_start: 0.7614 (mmm) cc_final: 0.7334 (mmm) outliers start: 10 outliers final: 7 residues processed: 286 average time/residue: 0.3567 time to fit residues: 143.0827 Evaluate side-chains 159 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0020 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 ASN B 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.134721 restraints weight = 98700.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127393 restraints weight = 95079.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124091 restraints weight = 88161.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125605 restraints weight = 71134.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126401 restraints weight = 55583.913| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17621 Z= 0.123 Angle : 0.624 10.024 23959 Z= 0.319 Chirality : 0.042 0.170 2730 Planarity : 0.005 0.056 3086 Dihedral : 6.406 65.458 2386 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 8.23 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.17), residues: 2181 helix: -0.29 (0.22), residues: 534 sheet: -1.25 (0.22), residues: 471 loop : -1.10 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 276 TYR 0.016 0.001 TYR A 991 PHE 0.021 0.001 PHE A 22 TRP 0.019 0.001 TRP C 13 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00274 (17613) covalent geometry : angle 0.61547 (23947) hydrogen bonds : bond 0.04516 ( 674) hydrogen bonds : angle 5.98556 ( 1890) metal coordination : bond 0.00591 ( 8) metal coordination : angle 4.60663 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7936 (ptm) cc_final: 0.7665 (ptm) REVERT: A 892 THR cc_start: 0.7168 (m) cc_final: 0.6888 (m) REVERT: A 1078 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6267 (tm-30) REVERT: A 1093 VAL cc_start: 0.9120 (m) cc_final: 0.8900 (p) REVERT: B 721 MET cc_start: 0.4251 (mpp) cc_final: 0.4024 (mmm) REVERT: D 327 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.5762 (tt0) REVERT: D 575 MET cc_start: 0.7416 (mmm) cc_final: 0.7139 (mmm) outliers start: 22 outliers final: 18 residues processed: 176 average time/residue: 0.3542 time to fit residues: 89.1778 Evaluate side-chains 158 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 561 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 153 optimal weight: 0.7980 chunk 20 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.167226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131844 restraints weight = 98844.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.121385 restraints weight = 84732.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121797 restraints weight = 87749.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122412 restraints weight = 57282.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122549 restraints weight = 49764.444| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17621 Z= 0.150 Angle : 0.580 8.520 23959 Z= 0.296 Chirality : 0.040 0.164 2730 Planarity : 0.005 0.065 3086 Dihedral : 5.968 67.133 2384 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.45 % Allowed : 8.64 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.17), residues: 2181 helix: 0.10 (0.22), residues: 534 sheet: -1.33 (0.22), residues: 494 loop : -0.99 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 392 TYR 0.016 0.001 TYR A 385 PHE 0.019 0.001 PHE B 627 TRP 0.017 0.001 TRP C 13 HIS 0.005 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00345 (17613) covalent geometry : angle 0.57368 (23947) hydrogen bonds : bond 0.04105 ( 674) hydrogen bonds : angle 5.58977 ( 1890) metal coordination : bond 0.00471 ( 8) metal coordination : angle 3.83242 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7839 (ptm) cc_final: 0.7541 (ptm) REVERT: A 1078 GLU cc_start: 0.6341 (tm-30) cc_final: 0.6106 (tm-30) REVERT: A 1087 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 1093 VAL cc_start: 0.9135 (m) cc_final: 0.8907 (p) REVERT: B 721 MET cc_start: 0.4084 (mpp) cc_final: 0.3655 (mmm) REVERT: D 209 HIS cc_start: 0.7225 (OUTLIER) cc_final: 0.6737 (p-80) REVERT: D 575 MET cc_start: 0.7473 (mmm) cc_final: 0.7218 (mmm) outliers start: 28 outliers final: 17 residues processed: 171 average time/residue: 0.3348 time to fit residues: 84.7277 Evaluate side-chains 148 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 209 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 127 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.163804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128013 restraints weight = 97897.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115117 restraints weight = 89516.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.115876 restraints weight = 87212.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116557 restraints weight = 57276.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116750 restraints weight = 54903.425| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17621 Z= 0.272 Angle : 0.642 6.454 23959 Z= 0.334 Chirality : 0.042 0.166 2730 Planarity : 0.005 0.056 3086 Dihedral : 5.836 71.624 2379 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.60 % Allowed : 9.58 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2181 helix: 0.29 (0.23), residues: 528 sheet: -1.65 (0.22), residues: 494 loop : -1.09 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.020 0.002 TYR A 385 PHE 0.017 0.002 PHE A 657 TRP 0.017 0.002 TRP C 13 HIS 0.007 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00634 (17613) covalent geometry : angle 0.63692 (23947) hydrogen bonds : bond 0.04346 ( 674) hydrogen bonds : angle 5.63227 ( 1890) metal coordination : bond 0.00575 ( 8) metal coordination : angle 3.62537 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7872 (ptm) cc_final: 0.7532 (ptm) REVERT: A 892 THR cc_start: 0.7256 (m) cc_final: 0.6972 (m) REVERT: A 926 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.7045 (mtm-85) REVERT: A 1078 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6108 (tm-30) REVERT: A 1087 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 1093 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8916 (p) REVERT: B 721 MET cc_start: 0.4142 (mpp) cc_final: 0.3781 (mmm) REVERT: D 209 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6762 (p-80) REVERT: D 327 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6189 (tt0) REVERT: D 575 MET cc_start: 0.7726 (mmm) cc_final: 0.7378 (mmm) outliers start: 31 outliers final: 20 residues processed: 161 average time/residue: 0.3406 time to fit residues: 81.1569 Evaluate side-chains 145 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 588 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.127343 restraints weight = 97884.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118678 restraints weight = 86574.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116367 restraints weight = 84763.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.117601 restraints weight = 62110.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118059 restraints weight = 49287.702| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17621 Z= 0.158 Angle : 0.565 5.975 23959 Z= 0.289 Chirality : 0.040 0.160 2730 Planarity : 0.004 0.058 3086 Dihedral : 5.506 64.631 2377 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.40 % Allowed : 10.77 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.18), residues: 2181 helix: 0.49 (0.23), residues: 535 sheet: -1.62 (0.22), residues: 487 loop : -1.03 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.016 0.001 TYR A 385 PHE 0.026 0.001 PHE D 315 TRP 0.016 0.001 TRP C 13 HIS 0.005 0.001 HIS A 968 Details of bonding type rmsd covalent geometry : bond 0.00371 (17613) covalent geometry : angle 0.56027 (23947) hydrogen bonds : bond 0.03712 ( 674) hydrogen bonds : angle 5.34183 ( 1890) metal coordination : bond 0.00402 ( 8) metal coordination : angle 3.27602 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7838 (ptm) cc_final: 0.7482 (ptm) REVERT: A 892 THR cc_start: 0.7248 (m) cc_final: 0.6989 (m) REVERT: A 926 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.7037 (mtm-85) REVERT: A 1078 GLU cc_start: 0.6199 (tm-30) cc_final: 0.5979 (tm-30) REVERT: A 1087 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 634 MET cc_start: 0.6636 (ppp) cc_final: 0.6396 (ppp) REVERT: B 721 MET cc_start: 0.4214 (mpp) cc_final: 0.3915 (mmm) REVERT: D 185 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5046 (t0) REVERT: D 209 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6741 (p-80) REVERT: D 575 MET cc_start: 0.7705 (mmm) cc_final: 0.7352 (mmm) outliers start: 27 outliers final: 20 residues processed: 147 average time/residue: 0.3256 time to fit residues: 70.6891 Evaluate side-chains 144 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 21 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.164755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.125799 restraints weight = 97499.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120090 restraints weight = 86890.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118420 restraints weight = 67484.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118605 restraints weight = 60368.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118644 restraints weight = 53319.818| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17621 Z= 0.158 Angle : 0.555 5.906 23959 Z= 0.284 Chirality : 0.040 0.159 2730 Planarity : 0.004 0.053 3086 Dihedral : 5.372 65.230 2377 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.76 % Allowed : 10.77 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.18), residues: 2181 helix: 0.68 (0.23), residues: 529 sheet: -1.69 (0.22), residues: 492 loop : -1.02 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 392 TYR 0.016 0.001 TYR A 385 PHE 0.033 0.001 PHE D 315 TRP 0.020 0.001 TRP A1143 HIS 0.004 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00372 (17613) covalent geometry : angle 0.55129 (23947) hydrogen bonds : bond 0.03559 ( 674) hydrogen bonds : angle 5.23523 ( 1890) metal coordination : bond 0.00356 ( 8) metal coordination : angle 3.07723 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7851 (ptm) cc_final: 0.7463 (ptm) REVERT: A 892 THR cc_start: 0.7188 (m) cc_final: 0.6922 (m) REVERT: A 903 LEU cc_start: 0.8735 (mt) cc_final: 0.8479 (mp) REVERT: A 991 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6623 (t80) REVERT: A 1087 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 721 MET cc_start: 0.4179 (mpp) cc_final: 0.3877 (mmm) REVERT: D 185 ASP cc_start: 0.6015 (OUTLIER) cc_final: 0.5169 (t0) REVERT: D 209 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6741 (p-80) REVERT: D 327 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6006 (tt0) REVERT: D 575 MET cc_start: 0.7706 (mmm) cc_final: 0.7364 (mmm) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.3208 time to fit residues: 72.3500 Evaluate side-chains 143 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 124 optimal weight: 0.0980 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.164505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129170 restraints weight = 98326.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121174 restraints weight = 88691.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118554 restraints weight = 85902.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119569 restraints weight = 63664.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119849 restraints weight = 52909.109| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17621 Z= 0.157 Angle : 0.548 6.503 23959 Z= 0.279 Chirality : 0.040 0.159 2730 Planarity : 0.004 0.051 3086 Dihedral : 5.285 65.905 2377 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.55 % Allowed : 11.44 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2181 helix: 0.74 (0.24), residues: 530 sheet: -1.71 (0.22), residues: 498 loop : -1.00 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 926 TYR 0.015 0.001 TYR B 694 PHE 0.014 0.001 PHE A1040 TRP 0.019 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00369 (17613) covalent geometry : angle 0.54393 (23947) hydrogen bonds : bond 0.03474 ( 674) hydrogen bonds : angle 5.15478 ( 1890) metal coordination : bond 0.00349 ( 8) metal coordination : angle 3.08736 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7763 (ptm) cc_final: 0.7449 (ptm) REVERT: A 892 THR cc_start: 0.7203 (m) cc_final: 0.6934 (m) REVERT: A 903 LEU cc_start: 0.8813 (mt) cc_final: 0.8579 (mp) REVERT: A 991 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 1087 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 721 MET cc_start: 0.4242 (mpp) cc_final: 0.3975 (mmm) REVERT: D 209 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6755 (p-80) REVERT: D 327 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6101 (tt0) REVERT: D 575 MET cc_start: 0.7657 (mmm) cc_final: 0.7351 (mmm) outliers start: 30 outliers final: 25 residues processed: 144 average time/residue: 0.3243 time to fit residues: 69.1678 Evaluate side-chains 144 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 145 optimal weight: 40.0000 chunk 153 optimal weight: 7.9990 chunk 57 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.165801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.132755 restraints weight = 97723.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125008 restraints weight = 95655.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123048 restraints weight = 84985.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.122744 restraints weight = 72189.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.123338 restraints weight = 64138.947| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17621 Z= 0.097 Angle : 0.525 5.903 23959 Z= 0.264 Chirality : 0.039 0.151 2730 Planarity : 0.004 0.050 3086 Dihedral : 5.025 62.178 2375 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.45 % Allowed : 11.44 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.18), residues: 2181 helix: 0.84 (0.24), residues: 531 sheet: -1.60 (0.22), residues: 494 loop : -0.92 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1102 TYR 0.013 0.001 TYR A 991 PHE 0.011 0.001 PHE A1040 TRP 0.023 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00228 (17613) covalent geometry : angle 0.52083 (23947) hydrogen bonds : bond 0.03113 ( 674) hydrogen bonds : angle 5.00851 ( 1890) metal coordination : bond 0.00263 ( 8) metal coordination : angle 2.91919 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7793 (ptm) cc_final: 0.7409 (ptm) REVERT: A 892 THR cc_start: 0.7133 (m) cc_final: 0.6869 (m) REVERT: A 903 LEU cc_start: 0.8725 (mt) cc_final: 0.8450 (mp) REVERT: A 991 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.6682 (t80) REVERT: A 1087 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8602 (p) REVERT: A 1093 VAL cc_start: 0.9130 (m) cc_final: 0.8875 (p) REVERT: B 721 MET cc_start: 0.4247 (mpp) cc_final: 0.4012 (mmm) REVERT: D 209 HIS cc_start: 0.7204 (OUTLIER) cc_final: 0.6714 (p-80) REVERT: D 258 MET cc_start: 0.4450 (ppp) cc_final: 0.3940 (ppp) REVERT: D 575 MET cc_start: 0.7516 (mmm) cc_final: 0.7242 (mmm) outliers start: 28 outliers final: 21 residues processed: 149 average time/residue: 0.3303 time to fit residues: 73.7437 Evaluate side-chains 143 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 149 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.163563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.123438 restraints weight = 97663.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121247 restraints weight = 94944.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.117598 restraints weight = 62120.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117447 restraints weight = 53073.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117561 restraints weight = 53687.165| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17621 Z= 0.210 Angle : 0.577 6.343 23959 Z= 0.294 Chirality : 0.040 0.162 2730 Planarity : 0.005 0.058 3086 Dihedral : 5.186 68.102 2375 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.66 % Allowed : 11.65 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2181 helix: 0.78 (0.24), residues: 531 sheet: -1.73 (0.22), residues: 500 loop : -1.02 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 287 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE A 657 TRP 0.022 0.001 TRP A1143 HIS 0.006 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00494 (17613) covalent geometry : angle 0.57302 (23947) hydrogen bonds : bond 0.03577 ( 674) hydrogen bonds : angle 5.13034 ( 1890) metal coordination : bond 0.00396 ( 8) metal coordination : angle 3.09316 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7839 (ptm) cc_final: 0.7490 (ptm) REVERT: A 892 THR cc_start: 0.7195 (m) cc_final: 0.6927 (m) REVERT: A 903 LEU cc_start: 0.8823 (mt) cc_final: 0.8518 (mp) REVERT: A 991 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6952 (t80) REVERT: A 1087 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8668 (p) REVERT: B 721 MET cc_start: 0.4163 (mpp) cc_final: 0.3940 (mmm) REVERT: D 209 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6756 (p-80) REVERT: D 258 MET cc_start: 0.4573 (ppp) cc_final: 0.4058 (ppp) REVERT: D 327 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6238 (tt0) REVERT: D 575 MET cc_start: 0.7646 (mmm) cc_final: 0.7353 (mmm) outliers start: 32 outliers final: 26 residues processed: 147 average time/residue: 0.3480 time to fit residues: 76.4930 Evaluate side-chains 146 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1078 GLU Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 588 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 203 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 ASN A 968 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.165264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.129839 restraints weight = 98148.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.115853 restraints weight = 82901.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116471 restraints weight = 71685.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.117080 restraints weight = 56897.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117412 restraints weight = 51020.678| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17621 Z= 0.102 Angle : 0.527 6.606 23959 Z= 0.264 Chirality : 0.039 0.152 2730 Planarity : 0.004 0.048 3086 Dihedral : 4.964 63.515 2375 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.40 % Allowed : 11.90 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.18), residues: 2181 helix: 0.91 (0.24), residues: 532 sheet: -1.63 (0.22), residues: 499 loop : -0.91 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.013 0.001 TYR A 991 PHE 0.011 0.001 PHE A1040 TRP 0.021 0.001 TRP A1143 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00239 (17613) covalent geometry : angle 0.52346 (23947) hydrogen bonds : bond 0.03079 ( 674) hydrogen bonds : angle 4.94150 ( 1890) metal coordination : bond 0.00261 ( 8) metal coordination : angle 2.89926 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 911 is missing expected H atoms. Skipping. Residue VAL 912 is missing expected H atoms. Skipping. Residue SER 914 is missing expected H atoms. Skipping. Residue LEU 915 is missing expected H atoms. Skipping. Residue MET 917 is missing expected H atoms. Skipping. Residue LYS 918 is missing expected H atoms. Skipping. Residue LEU 919 is missing expected H atoms. Skipping. Residue THR 922 is missing expected H atoms. Skipping. Residue MET 925 is missing expected H atoms. Skipping. Residue SER 303 is missing expected H atoms. Skipping. Residue VAL 305 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7907 (ptm) cc_final: 0.7466 (ptm) REVERT: A 593 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8686 (t) REVERT: A 892 THR cc_start: 0.7091 (m) cc_final: 0.6830 (m) REVERT: A 991 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 1087 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 2 MET cc_start: 0.7025 (ppp) cc_final: 0.5868 (ppp) REVERT: D 209 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6780 (p-80) REVERT: D 258 MET cc_start: 0.4656 (ppp) cc_final: 0.4121 (ppp) REVERT: D 575 MET cc_start: 0.7587 (mmm) cc_final: 0.7294 (mmm) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.3481 time to fit residues: 76.5877 Evaluate side-chains 146 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 650 CYS Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1083 GLU Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1186 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 723 LYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 209 HIS Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 115 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 213 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.163956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.127817 restraints weight = 97400.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.112987 restraints weight = 85246.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114725 restraints weight = 71148.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115069 restraints weight = 56649.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115388 restraints weight = 50575.935| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17621 Z= 0.171 Angle : 0.550 6.665 23959 Z= 0.279 Chirality : 0.040 0.159 2730 Planarity : 0.004 0.044 3086 Dihedral : 5.040 67.268 2375 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.45 % Allowed : 11.90 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.18), residues: 2181 helix: 0.90 (0.24), residues: 532 sheet: -1.69 (0.22), residues: 503 loop : -0.98 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A1040 TRP 0.020 0.001 TRP A1143 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00404 (17613) covalent geometry : angle 0.54640 (23947) hydrogen bonds : bond 0.03330 ( 674) hydrogen bonds : angle 4.98761 ( 1890) metal coordination : bond 0.00337 ( 8) metal coordination : angle 2.97262 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5107.57 seconds wall clock time: 88 minutes 31.09 seconds (5311.09 seconds total)