Starting phenix.real_space_refine on Wed May 8 04:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/05_2024/8wp0_37705_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.105 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 P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 5976 2.51 5 N 1595 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 9372 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9308 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.45, per 1000 atoms: 0.58 Number of scatterers: 9372 At special positions: 0 Unit cell: (72.6, 106.7, 144.1, 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) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1755 8.00 N 1595 7.00 C 5976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 2.2 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 4 sheets defined 42.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 37 through 43 removed outlier: 4.279A pdb=" N PHE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 52 through 71 removed outlier: 4.006A pdb=" N MET A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 4.392A pdb=" N PHE A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 62 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 63 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 64 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 67 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 71 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.627A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 removed outlier: 3.912A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.754A pdb=" N VAL A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 183 removed outlier: 3.564A pdb=" N TYR A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 193 through 199 removed outlier: 4.200A pdb=" N GLY A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 220 removed outlier: 3.682A pdb=" N THR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.639A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.888A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 4.037A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 removed outlier: 3.690A pdb=" N CYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.752A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 325 removed outlier: 3.577A pdb=" N LEU A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.866A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 471 through 480 removed outlier: 4.055A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.593A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 596 through 604 removed outlier: 3.520A pdb=" N GLU A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.922A pdb=" N HIS A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.654A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.298A pdb=" N GLY A 690 " --> pdb=" O TYR A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 Proline residue: A 702 - end of helix removed outlier: 3.552A pdb=" N ALA A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 750 removed outlier: 3.505A pdb=" N TYR A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 743 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.620A pdb=" N ARG A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 779 No H-bonds generated for 'chain 'A' and resid 776 through 779' Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 809 through 812 No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 832 through 852 Proline residue: A 841 - end of helix removed outlier: 3.795A pdb=" N ASN A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.911A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 867 through 872' Processing helix chain 'A' and resid 879 through 886 removed outlier: 3.850A pdb=" N ALA A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 891 No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 901 through 920 removed outlier: 3.577A pdb=" N TYR A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 925 No H-bonds generated for 'chain 'A' and resid 922 through 925' Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.716A pdb=" N LEU A 932 " --> pdb=" O GLU A 928 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 966 removed outlier: 4.031A pdb=" N ALA A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 974 removed outlier: 3.934A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 974' Processing helix chain 'A' and resid 1055 through 1058 No H-bonds generated for 'chain 'A' and resid 1055 through 1058' Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1118 through 1122 Processing helix chain 'A' and resid 1128 through 1132 Processing helix chain 'A' and resid 1151 through 1164 removed outlier: 3.676A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1193 No H-bonds generated for 'chain 'A' and resid 1190 through 1193' Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.786A pdb=" N LEU A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.567A pdb=" N GLU A 366 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 425 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 368 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN A 423 " --> pdb=" O LYS A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.951A pdb=" N ILE A 524 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A 554 " --> pdb=" O LEU A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 645 through 647 removed outlier: 3.814A pdb=" N GLU A 655 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 6.813A pdb=" N VAL A1169 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR A1199 " --> pdb=" O LEU A1170 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 171 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3036 1.34 - 1.46: 1984 1.46 - 1.58: 4450 1.58 - 1.69: 10 1.69 - 1.81: 67 Bond restraints: 9547 Sorted by residual: bond pdb=" C4 ATP A1303 " pdb=" C5 ATP A1303 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.27e+01 bond pdb=" C5 ATP A1303 " pdb=" C6 ATP A1303 " ideal model delta sigma weight residual 1.409 1.497 -0.088 1.00e-02 1.00e+04 7.72e+01 bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP A1301 " pdb=" N7 ATP A1301 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 9542 not shown) Histogram of bond angle deviations from ideal: 80.10 - 92.38: 2 92.38 - 104.67: 116 104.67 - 116.96: 6337 116.96 - 129.25: 6429 129.25 - 141.54: 51 Bond angle restraints: 12935 Sorted by residual: angle pdb=" C ALA A 858 " pdb=" CA ALA A 858 " pdb=" CB ALA A 858 " ideal model delta sigma weight residual 111.72 80.10 31.62 1.53e+00 4.27e-01 4.27e+02 angle pdb=" PB ATP A1303 " pdb=" O3B ATP A1303 " pdb=" PG ATP A1303 " ideal model delta sigma weight residual 139.87 121.66 18.21 1.00e+00 1.00e+00 3.31e+02 angle pdb=" N GLY A 859 " pdb=" CA GLY A 859 " pdb=" C GLY A 859 " ideal model delta sigma weight residual 111.36 131.39 -20.03 1.17e+00 7.31e-01 2.93e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 121.87 14.96 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 125.15 14.72 1.00e+00 1.00e+00 2.17e+02 ... (remaining 12930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5414 16.88 - 33.77: 221 33.77 - 50.65: 44 50.65 - 67.53: 3 67.53 - 84.42: 13 Dihedral angle restraints: 5695 sinusoidal: 2207 harmonic: 3488 Sorted by residual: dihedral pdb=" C ALA A 858 " pdb=" N ALA A 858 " pdb=" CA ALA A 858 " pdb=" CB ALA A 858 " ideal model delta harmonic sigma weight residual -122.60 -84.68 -37.92 0 2.50e+00 1.60e-01 2.30e+02 dihedral pdb=" C SER A 681 " pdb=" N SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual -122.60 -152.43 29.83 0 2.50e+00 1.60e-01 1.42e+02 dihedral pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual 122.80 148.70 -25.90 0 2.50e+00 1.60e-01 1.07e+02 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 1483 0.249 - 0.498: 1 0.498 - 0.747: 1 0.747 - 0.996: 0 0.996 - 1.245: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA SER A 681 " pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CB SER A 681 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" CA ALA A 858 " pdb=" N ALA A 858 " pdb=" C ALA A 858 " pdb=" CB ALA A 858 " both_signs ideal model delta sigma weight residual False 2.48 3.06 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CA GLU A 449 " pdb=" N GLU A 449 " pdb=" C GLU A 449 " pdb=" CB GLU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1483 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A1303 " 0.009 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" C2 ATP A1303 " 0.003 2.00e-02 2.50e+03 pdb=" C4 ATP A1303 " -0.003 2.00e-02 2.50e+03 pdb=" C5 ATP A1303 " -0.056 2.00e-02 2.50e+03 pdb=" C6 ATP A1303 " 0.007 2.00e-02 2.50e+03 pdb=" C8 ATP A1303 " -0.002 2.00e-02 2.50e+03 pdb=" N1 ATP A1303 " 0.008 2.00e-02 2.50e+03 pdb=" N3 ATP A1303 " 0.000 2.00e-02 2.50e+03 pdb=" N6 ATP A1303 " 0.007 2.00e-02 2.50e+03 pdb=" N7 ATP A1303 " 0.028 2.00e-02 2.50e+03 pdb=" N9 ATP A1303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.32e+00 pdb=" N PRO A 702 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 449 " -0.043 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 450 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.037 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 3 2.08 - 2.79: 2307 2.79 - 3.49: 11344 3.49 - 4.20: 20847 4.20 - 4.90: 36008 Nonbonded interactions: 70509 Sorted by model distance: nonbonded pdb=" CB ALA A 454 " pdb=" NH1 ARG A 653 " model vdw 1.379 3.540 nonbonded pdb=" O ALA A 858 " pdb=" CB ALA A 858 " model vdw 1.932 2.768 nonbonded pdb=" CZ TYR A1019 " pdb=" N7 ATP A1303 " model vdw 2.072 2.672 nonbonded pdb=" O1B ATP A1303 " pdb="MG MG A1304 " model vdw 2.141 2.170 nonbonded pdb=" O2G ATP A1303 " pdb="MG MG A1304 " model vdw 2.285 2.170 ... (remaining 70504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.200 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9547 Z= 0.311 Angle : 1.106 31.625 12935 Z= 0.705 Chirality : 0.063 1.245 1486 Planarity : 0.006 0.068 1640 Dihedral : 11.225 84.417 3467 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.50 (0.15), residues: 1213 helix: -4.85 (0.06), residues: 689 sheet: -2.87 (0.51), residues: 87 loop : -3.25 (0.23), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 933 HIS 0.006 0.001 HIS A 937 PHE 0.020 0.002 PHE A 752 TYR 0.015 0.002 TYR A1019 ARG 0.007 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7978 (mttp) cc_final: 0.7585 (mmtt) REVERT: A 251 SER cc_start: 0.8596 (m) cc_final: 0.8368 (p) REVERT: A 365 ILE cc_start: 0.8373 (mm) cc_final: 0.8149 (mm) REVERT: A 961 ASN cc_start: 0.8611 (t0) cc_final: 0.8184 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3096 time to fit residues: 75.1167 Evaluate side-chains 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 350 GLN A 442 GLN A 448 GLN A 585 HIS A 602 GLN A 748 GLN A 758 ASN A 784 HIS A 878 ASN A1039 HIS A1041 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9547 Z= 0.446 Angle : 0.739 8.363 12935 Z= 0.397 Chirality : 0.047 0.162 1486 Planarity : 0.006 0.052 1640 Dihedral : 9.521 81.455 1390 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.84 % Allowed : 6.84 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.48 (0.18), residues: 1213 helix: -3.98 (0.12), residues: 680 sheet: -2.42 (0.56), residues: 76 loop : -2.95 (0.24), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 933 HIS 0.004 0.001 HIS A1128 PHE 0.036 0.003 PHE A 69 TYR 0.016 0.002 TYR A1019 ARG 0.007 0.001 ARG A1211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.092 Fit side-chains REVERT: A 22 GLN cc_start: 0.7759 (mm110) cc_final: 0.7501 (tp40) REVERT: A 35 LYS cc_start: 0.7928 (mttp) cc_final: 0.7722 (mtmm) REVERT: A 381 MET cc_start: 0.7815 (tpp) cc_final: 0.7490 (mpp) REVERT: A 456 THR cc_start: 0.8863 (p) cc_final: 0.8517 (t) REVERT: A 604 MET cc_start: 0.5346 (ptt) cc_final: 0.4877 (mtp) REVERT: A 711 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7744 (mtm) REVERT: A 961 ASN cc_start: 0.8647 (t0) cc_final: 0.8218 (t0) REVERT: A 975 ARG cc_start: 0.8302 (tmm-80) cc_final: 0.7861 (ttp-170) outliers start: 18 outliers final: 7 residues processed: 120 average time/residue: 0.2733 time to fit residues: 43.9014 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 ASN A 850 GLN A 921 GLN A1080 ASN A1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9547 Z= 0.162 Angle : 0.577 10.339 12935 Z= 0.308 Chirality : 0.041 0.145 1486 Planarity : 0.004 0.044 1640 Dihedral : 8.793 82.846 1390 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.02 % Allowed : 9.60 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.19), residues: 1213 helix: -3.33 (0.15), residues: 663 sheet: -1.79 (0.65), residues: 66 loop : -2.74 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.000 HIS A1128 PHE 0.018 0.001 PHE A 485 TYR 0.013 0.001 TYR A1019 ARG 0.005 0.000 ARG A1223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.082 Fit side-chains REVERT: A 22 GLN cc_start: 0.7743 (mm110) cc_final: 0.7482 (tp40) REVERT: A 35 LYS cc_start: 0.8001 (mttp) cc_final: 0.7747 (mtmm) REVERT: A 604 MET cc_start: 0.5334 (ptt) cc_final: 0.4872 (mtp) REVERT: A 961 ASN cc_start: 0.8601 (t0) cc_final: 0.8166 (t0) REVERT: A 975 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.7907 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.2736 time to fit residues: 40.6648 Evaluate side-chains 97 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 972 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A1128 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9547 Z= 0.247 Angle : 0.588 6.964 12935 Z= 0.313 Chirality : 0.043 0.183 1486 Planarity : 0.004 0.039 1640 Dihedral : 8.547 86.058 1390 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.53 % Allowed : 10.32 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.20), residues: 1213 helix: -2.93 (0.16), residues: 661 sheet: -1.69 (0.67), residues: 65 loop : -2.65 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.001 HIS A1128 PHE 0.024 0.002 PHE A 69 TYR 0.015 0.001 TYR A 740 ARG 0.006 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.967 Fit side-chains REVERT: A 22 GLN cc_start: 0.7799 (mm110) cc_final: 0.7485 (tp40) REVERT: A 35 LYS cc_start: 0.8004 (mttp) cc_final: 0.7500 (mmtt) REVERT: A 470 MET cc_start: 0.7327 (tpp) cc_final: 0.7042 (tpt) REVERT: A 485 PHE cc_start: 0.8164 (t80) cc_final: 0.7881 (t80) REVERT: A 604 MET cc_start: 0.5573 (ptt) cc_final: 0.5098 (mtp) REVERT: A 961 ASN cc_start: 0.8628 (t0) cc_final: 0.8171 (t0) REVERT: A 975 ARG cc_start: 0.8304 (tmm-80) cc_final: 0.7982 (ttm170) REVERT: A 1007 ARG cc_start: 0.6983 (ptt90) cc_final: 0.6525 (ptt90) REVERT: A 1094 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6655 (tm-30) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.2491 time to fit residues: 38.7451 Evaluate side-chains 106 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9547 Z= 0.255 Angle : 0.588 10.317 12935 Z= 0.311 Chirality : 0.043 0.150 1486 Planarity : 0.003 0.040 1640 Dihedral : 8.366 88.051 1390 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.15 % Allowed : 10.83 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.21), residues: 1213 helix: -2.64 (0.17), residues: 645 sheet: -1.91 (0.61), residues: 75 loop : -2.50 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.001 HIS A1128 PHE 0.026 0.002 PHE A 372 TYR 0.016 0.001 TYR A 740 ARG 0.007 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.110 Fit side-chains REVERT: A 22 GLN cc_start: 0.7851 (mm110) cc_final: 0.7484 (tp40) REVERT: A 35 LYS cc_start: 0.8028 (mttp) cc_final: 0.7785 (mtmm) REVERT: A 55 MET cc_start: 0.7995 (tpp) cc_final: 0.7700 (tpp) REVERT: A 456 THR cc_start: 0.8870 (p) cc_final: 0.8500 (t) REVERT: A 604 MET cc_start: 0.5812 (ptt) cc_final: 0.5425 (mtp) REVERT: A 622 ARG cc_start: 0.4793 (ptt-90) cc_final: 0.4497 (ptt-90) REVERT: A 653 ARG cc_start: 0.7327 (mtm180) cc_final: 0.7071 (mtm180) REVERT: A 961 ASN cc_start: 0.8631 (t0) cc_final: 0.8199 (t0) REVERT: A 975 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.8011 (ttm170) REVERT: A 1007 ARG cc_start: 0.7012 (ptt90) cc_final: 0.6527 (ptt90) REVERT: A 1094 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6672 (tm-30) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.2511 time to fit residues: 40.4959 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0870 chunk 112 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9547 Z= 0.149 Angle : 0.531 7.026 12935 Z= 0.283 Chirality : 0.041 0.147 1486 Planarity : 0.003 0.039 1640 Dihedral : 8.061 89.124 1390 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.84 % Allowed : 11.75 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.22), residues: 1213 helix: -2.35 (0.18), residues: 646 sheet: -1.92 (0.62), residues: 77 loop : -2.35 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.020 0.001 PHE A 372 TYR 0.014 0.001 TYR A 740 ARG 0.005 0.000 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7763 (mm110) cc_final: 0.7440 (tp40) REVERT: A 35 LYS cc_start: 0.8029 (mttp) cc_final: 0.7806 (mtmm) REVERT: A 470 MET cc_start: 0.7481 (tpp) cc_final: 0.7196 (tpt) REVERT: A 604 MET cc_start: 0.5964 (ptt) cc_final: 0.5390 (mtp) REVERT: A 622 ARG cc_start: 0.4861 (ptt-90) cc_final: 0.4532 (ptt-90) REVERT: A 653 ARG cc_start: 0.7333 (mtm180) cc_final: 0.6180 (mtm110) REVERT: A 961 ASN cc_start: 0.8605 (t0) cc_final: 0.8185 (t0) REVERT: A 975 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.8001 (ttm170) REVERT: A 1007 ARG cc_start: 0.6960 (ptt90) cc_final: 0.6477 (ptt90) REVERT: A 1161 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6506 (mtt90) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 0.2596 time to fit residues: 39.4467 Evaluate side-chains 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1161 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9547 Z= 0.198 Angle : 0.561 10.833 12935 Z= 0.294 Chirality : 0.042 0.151 1486 Planarity : 0.003 0.039 1640 Dihedral : 7.993 89.027 1390 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.84 % Allowed : 12.46 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.22), residues: 1213 helix: -2.15 (0.19), residues: 646 sheet: -1.82 (0.61), residues: 78 loop : -2.32 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.016 0.001 PHE A 372 TYR 0.015 0.001 TYR A 740 ARG 0.005 0.000 ARG A1198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7804 (mm110) cc_final: 0.7466 (tp40) REVERT: A 35 LYS cc_start: 0.8086 (mttp) cc_final: 0.7822 (mtmm) REVERT: A 470 MET cc_start: 0.7417 (tpp) cc_final: 0.7134 (tpt) REVERT: A 604 MET cc_start: 0.5910 (ptt) cc_final: 0.5368 (mtp) REVERT: A 622 ARG cc_start: 0.4831 (ptt-90) cc_final: 0.4514 (ptt-90) REVERT: A 961 ASN cc_start: 0.8623 (t0) cc_final: 0.8212 (t0) REVERT: A 975 ARG cc_start: 0.8309 (tmm-80) cc_final: 0.8047 (ttm170) REVERT: A 1007 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6421 (ptt90) REVERT: A 1161 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6572 (mtt90) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.2890 time to fit residues: 43.6913 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1161 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9547 Z= 0.192 Angle : 0.567 11.892 12935 Z= 0.291 Chirality : 0.042 0.159 1486 Planarity : 0.003 0.039 1640 Dihedral : 7.884 87.858 1390 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.74 % Allowed : 12.46 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.22), residues: 1213 helix: -2.01 (0.19), residues: 649 sheet: -1.68 (0.62), residues: 78 loop : -2.27 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.021 0.001 PHE A 309 TYR 0.015 0.001 TYR A 740 ARG 0.005 0.000 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7874 (mm110) cc_final: 0.7496 (tp40) REVERT: A 35 LYS cc_start: 0.8065 (mttp) cc_final: 0.7756 (mtmm) REVERT: A 456 THR cc_start: 0.8894 (p) cc_final: 0.8502 (t) REVERT: A 470 MET cc_start: 0.7520 (tpp) cc_final: 0.7295 (tpt) REVERT: A 604 MET cc_start: 0.5897 (ptt) cc_final: 0.5367 (mtp) REVERT: A 622 ARG cc_start: 0.4818 (ptt-90) cc_final: 0.4506 (ptt-90) REVERT: A 961 ASN cc_start: 0.8618 (t0) cc_final: 0.8227 (t0) REVERT: A 975 ARG cc_start: 0.8329 (tmm-80) cc_final: 0.8081 (ttm170) REVERT: A 1007 ARG cc_start: 0.6921 (ptt90) cc_final: 0.6397 (ptt90) REVERT: A 1161 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6560 (mtt90) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.2910 time to fit residues: 41.1918 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9547 Z= 0.163 Angle : 0.548 10.700 12935 Z= 0.282 Chirality : 0.041 0.167 1486 Planarity : 0.003 0.038 1640 Dihedral : 7.709 86.761 1390 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.74 % Allowed : 12.46 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1213 helix: -1.84 (0.20), residues: 648 sheet: -1.52 (0.63), residues: 78 loop : -2.23 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.020 0.001 PHE A 309 TYR 0.014 0.001 TYR A 740 ARG 0.008 0.000 ARG A1223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.193 Fit side-chains REVERT: A 22 GLN cc_start: 0.7868 (mm110) cc_final: 0.7514 (tp40) REVERT: A 35 LYS cc_start: 0.8106 (mttp) cc_final: 0.7760 (mtmm) REVERT: A 456 THR cc_start: 0.8893 (p) cc_final: 0.8509 (t) REVERT: A 604 MET cc_start: 0.5891 (ptt) cc_final: 0.5370 (mtp) REVERT: A 622 ARG cc_start: 0.4705 (ptt-90) cc_final: 0.4390 (ptt-90) REVERT: A 961 ASN cc_start: 0.8573 (t0) cc_final: 0.8215 (t0) REVERT: A 975 ARG cc_start: 0.8318 (tmm-80) cc_final: 0.8099 (ttm170) REVERT: A 1007 ARG cc_start: 0.6920 (ptt90) cc_final: 0.6383 (ptt90) REVERT: A 1161 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6291 (mtt90) outliers start: 17 outliers final: 16 residues processed: 107 average time/residue: 0.2925 time to fit residues: 41.7396 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9547 Z= 0.135 Angle : 0.538 10.618 12935 Z= 0.275 Chirality : 0.040 0.155 1486 Planarity : 0.003 0.037 1640 Dihedral : 7.545 85.871 1390 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.43 % Allowed : 12.77 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 1213 helix: -1.63 (0.20), residues: 643 sheet: -1.38 (0.64), residues: 78 loop : -2.21 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.018 0.001 PHE A 309 TYR 0.013 0.001 TYR A 740 ARG 0.006 0.000 ARG A1211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.071 Fit side-chains REVERT: A 35 LYS cc_start: 0.8081 (mttp) cc_final: 0.7765 (mtmm) REVERT: A 456 THR cc_start: 0.8887 (p) cc_final: 0.8507 (t) REVERT: A 604 MET cc_start: 0.5967 (ptt) cc_final: 0.5414 (mtp) REVERT: A 622 ARG cc_start: 0.4743 (ptt-90) cc_final: 0.4436 (ptt-90) REVERT: A 961 ASN cc_start: 0.8596 (t0) cc_final: 0.8231 (t0) REVERT: A 1007 ARG cc_start: 0.6776 (ptt90) cc_final: 0.6189 (ptt90) REVERT: A 1161 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6969 (mtm180) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.2688 time to fit residues: 36.5377 Evaluate side-chains 105 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.175413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121474 restraints weight = 11372.005| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.94 r_work: 0.3013 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9547 Z= 0.164 Angle : 0.551 10.139 12935 Z= 0.281 Chirality : 0.041 0.157 1486 Planarity : 0.003 0.034 1640 Dihedral : 7.513 85.997 1390 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.74 % Allowed : 12.77 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1213 helix: -1.57 (0.20), residues: 651 sheet: -1.46 (0.59), residues: 88 loop : -2.21 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 684 HIS 0.002 0.000 HIS A1128 PHE 0.018 0.001 PHE A 309 TYR 0.014 0.001 TYR A 740 ARG 0.010 0.000 ARG A1193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.18 seconds wall clock time: 41 minutes 45.88 seconds (2505.88 seconds total)