Starting phenix.real_space_refine on Mon Aug 25 19:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762.map" model { file = "/net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr4_37762/08_2025/8wr4_37762_neut.cif" } resolution = 3.07 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= 0.001 sd= 0.020 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 282 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 18267 2.51 5 N 5239 2.21 5 O 6405 1.98 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30250 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10106 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 bond proxies already assigned to first conformer: 10300 Chain: "B" Number of atoms: 11993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1442, 11993 Classifications: {'peptide': 1442} Link IDs: {'PTRANS': 39, 'TRANS': 1402} Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 858 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1108 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1108 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "N" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 2192 Classifications: {'RNA': 103} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 43} Link IDs: {'rna2p': 9, 'rna3p': 93} Chain breaks: 1 Chain: "O" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2129 Classifications: {'RNA': 100} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 51, 'rna3p_pyr': 42} Link IDs: {'rna2p': 6, 'rna3p': 93} Chain breaks: 1 Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 754 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP A 672 " occ=0.46 ... (14 atoms not shown) pdb=" OD2BASP A 672 " occ=0.54 Time building chain proxies: 8.63, per 1000 atoms: 0.29 Number of scatterers: 30250 At special positions: 0 Unit cell: (115.828, 158.045, 212.17, 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 55 16.00 P 282 15.00 Mg 2 11.99 O 6405 8.00 N 5239 7.00 C 18267 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 - 3.00 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5586 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 35 sheets defined 47.5% alpha, 12.0% beta 101 base pairs and 172 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.503A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 89 removed outlier: 3.912A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 removed outlier: 3.523A pdb=" N GLN A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 162 removed outlier: 4.119A pdb=" N HIS A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.681A pdb=" N SER A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 317 through 336 removed outlier: 4.181A pdb=" N TYR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.519A pdb=" N ASP A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.569A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 452 through 465 removed outlier: 3.851A pdb=" N PHE A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.774A pdb=" N PHE A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.872A pdb=" N THR A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 557 through 564 removed outlier: 4.101A pdb=" N LYS A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 588 Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.856A pdb=" N TYR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 619 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.666A pdb=" N PHE A 635 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.834A pdb=" N LEU A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 removed outlier: 3.507A pdb=" N GLU A 684 " --> pdb=" O ASN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 943 removed outlier: 3.946A pdb=" N TYR A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 976 Processing helix chain 'A' and resid 977 through 998 Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1025 through 1029 removed outlier: 3.581A pdb=" N ARG A1028 " --> pdb=" O SER A1025 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A1029 " --> pdb=" O LYS A1026 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1025 through 1029' Processing helix chain 'A' and resid 1030 through 1031 No H-bonds generated for 'chain 'A' and resid 1030 through 1031' Processing helix chain 'A' and resid 1032 through 1044 Processing helix chain 'A' and resid 1045 through 1054 removed outlier: 3.524A pdb=" N VAL A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1070 removed outlier: 4.059A pdb=" N ARG A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP A1065 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU A1066 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1112 Processing helix chain 'A' and resid 1193 through 1198 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1225 through 1235 Processing helix chain 'A' and resid 1236 through 1240 Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 4.102A pdb=" N LYS A1269 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1309 Processing helix chain 'A' and resid 1353 through 1359 Processing helix chain 'A' and resid 1410 through 1415 removed outlier: 4.159A pdb=" N THR A1414 " --> pdb=" O ARG A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1440 removed outlier: 4.014A pdb=" N PHE A1438 " --> pdb=" O ILE A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 58 through 88 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.845A pdb=" N HIS B 157 " --> pdb=" O TRP B 153 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.069A pdb=" N ILE B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 317 through 334 removed outlier: 4.174A pdb=" N TYR B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 6.848A pdb=" N GLU B 338 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 356 through 365 removed outlier: 4.123A pdb=" N LYS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.597A pdb=" N PHE B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.763A pdb=" N PHE B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.653A pdb=" N PHE B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 509 Processing helix chain 'B' and resid 520 through 534 removed outlier: 3.786A pdb=" N VAL B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 554 through 564 removed outlier: 4.563A pdb=" N LYS B 564 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 588 Proline residue: B 585 - end of helix removed outlier: 3.650A pdb=" N ARG B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 599 through 611 Processing helix chain 'B' and resid 619 through 625 removed outlier: 4.179A pdb=" N LYS B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.507A pdb=" N GLN B 636 " --> pdb=" O ASN B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 Processing helix chain 'B' and resid 662 through 673 removed outlier: 3.714A pdb=" N LEU B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 703 Processing helix chain 'B' and resid 717 through 722 removed outlier: 3.544A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 722' Processing helix chain 'B' and resid 723 through 752 removed outlier: 3.846A pdb=" N LYS B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN B 732 " --> pdb=" O LYS B 728 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.540A pdb=" N GLN B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.569A pdb=" N LYS B 791 " --> pdb=" O ASP B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 810 Processing helix chain 'B' and resid 848 through 852 Processing helix chain 'B' and resid 857 through 864 removed outlier: 4.554A pdb=" N ASP B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.757A pdb=" N ILE B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 903 removed outlier: 4.321A pdb=" N ASP B 898 " --> pdb=" O GLU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.793A pdb=" N LEU B 915 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 927 removed outlier: 3.658A pdb=" N GLN B 927 " --> pdb=" O MET B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 947 removed outlier: 3.795A pdb=" N ASN B 944 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 976 removed outlier: 3.872A pdb=" N THR B 969 " --> pdb=" O ASN B 965 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 971 " --> pdb=" O LYS B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 998 Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 1017 through 1021 Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.725A pdb=" N ILE B1029 " --> pdb=" O LYS B1026 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B1030 " --> pdb=" O LYS B1027 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1031 " --> pdb=" O ARG B1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1026 through 1031' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.664A pdb=" N ALA B1044 " --> pdb=" O VAL B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1053 Processing helix chain 'B' and resid 1062 through 1071 Processing helix chain 'B' and resid 1101 through 1112 Processing helix chain 'B' and resid 1193 through 1198 removed outlier: 3.548A pdb=" N GLY B1198 " --> pdb=" O LEU B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1216 Processing helix chain 'B' and resid 1219 through 1224 Processing helix chain 'B' and resid 1225 through 1235 Processing helix chain 'B' and resid 1236 through 1241 removed outlier: 3.643A pdb=" N TYR B1239 " --> pdb=" O ILE B1236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B1241 " --> pdb=" O LYS B1238 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1270 removed outlier: 3.878A pdb=" N LYS B1269 " --> pdb=" O GLY B1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1309 removed outlier: 3.664A pdb=" N VAL B1303 " --> pdb=" O PRO B1299 " (cutoff:3.500A) Processing helix chain 'B' and resid 1353 through 1359 Processing helix chain 'B' and resid 1395 through 1399 removed outlier: 3.567A pdb=" N LYS B1399 " --> pdb=" O SER B1396 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1415 removed outlier: 4.231A pdb=" N THR B1414 " --> pdb=" O ARG B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1432 through 1440 Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.630A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 39 through 53 Processing helix chain 'G' and resid 57 through 72 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.774A pdb=" N LEU H 13 " --> pdb=" O ASP H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 57 through 72 Processing helix chain 'H' and resid 81 through 93 removed outlier: 3.821A pdb=" N GLN H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 removed outlier: 6.601A pdb=" N ILE A 15 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER A 36 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP A 17 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A 34 " --> pdb=" O TRP A 17 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 19 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 205 removed outlier: 3.503A pdb=" N SER A 252 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 254 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 215 removed outlier: 6.447A pdb=" N LEU A 221 " --> pdb=" O SER A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 400 removed outlier: 4.729A pdb=" N LEU A 412 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LEU A 395 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N GLN A 410 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N PHE A 397 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 10.760A pdb=" N HIS A 408 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA7, first strand: chain 'A' and resid 468 through 469 removed outlier: 3.558A pdb=" N VAL A 469 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AA9, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AB1, first strand: chain 'A' and resid 1124 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1130 through 1137 Processing sheet with id=AB3, first strand: chain 'A' and resid 1166 through 1167 Processing sheet with id=AB4, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AB5, first strand: chain 'A' and resid 1293 through 1298 removed outlier: 4.858A pdb=" N PHE A1282 " --> pdb=" O ILE A1298 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU A1287 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU A1324 " --> pdb=" O GLU A1287 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A1322 " --> pdb=" O ASN A1318 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A1318 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1370 through 1375 removed outlier: 6.993A pdb=" N GLU A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR A1366 " --> pdb=" O GLU A1370 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR A1372 " --> pdb=" O GLU A1364 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A1333 " --> pdb=" O ILE A1418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 961 through 963 removed outlier: 6.755A pdb=" N ILE B 712 " --> pdb=" O VAL B 962 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 15 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 36 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP B 17 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 34 " --> pdb=" O TRP B 17 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 19 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN B 28 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AB9, first strand: chain 'B' and resid 219 through 226 removed outlier: 10.217A pdb=" N LYS B 219 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLY B 213 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU B 221 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP B 211 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASP B 223 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE B 209 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR B 225 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 249 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 204 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 264 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 398 through 400 Processing sheet with id=AC2, first strand: chain 'B' and resid 437 through 438 Processing sheet with id=AC3, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AC4, first strand: chain 'B' and resid 833 through 836 Processing sheet with id=AC5, first strand: chain 'B' and resid 879 through 881 Processing sheet with id=AC6, first strand: chain 'B' and resid 1003 through 1006 Processing sheet with id=AC7, first strand: chain 'B' and resid 1074 through 1079 Processing sheet with id=AC8, first strand: chain 'B' and resid 1124 through 1126 Processing sheet with id=AC9, first strand: chain 'B' and resid 1130 through 1137 Processing sheet with id=AD1, first strand: chain 'B' and resid 1166 through 1167 Processing sheet with id=AD2, first strand: chain 'B' and resid 1260 through 1261 Processing sheet with id=AD3, first strand: chain 'B' and resid 1293 through 1297 removed outlier: 6.175A pdb=" N PHE B1283 " --> pdb=" O ASP B1327 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP B1327 " --> pdb=" O PHE B1283 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1285 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1370 through 1375 removed outlier: 3.837A pdb=" N LYS B1365 " --> pdb=" O TYR B1372 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B1374 " --> pdb=" O VAL B1363 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL B1363 " --> pdb=" O VAL B1374 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B1333 " --> pdb=" O ILE B1418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 6 through 7 removed outlier: 6.355A pdb=" N LEU G 114 " --> pdb=" O VAL G 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD7, first strand: chain 'H' and resid 6 through 8 removed outlier: 6.907A pdb=" N ALA H 7 " --> pdb=" O LEU H 115 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 37 through 39 removed outlier: 6.808A pdb=" N VAL H 38 " --> pdb=" O LEU H 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 1004 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 246 hydrogen bonds 464 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 172 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4920 1.33 - 1.45: 9511 1.45 - 1.57: 16360 1.57 - 1.69: 558 1.69 - 1.81: 91 Bond restraints: 31440 Sorted by residual: bond pdb=" CD GLN A 306 " pdb=" OE1 GLN A 306 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.60e+01 bond pdb=" CG ASN A1006 " pdb=" OD1 ASN A1006 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.56e+01 bond pdb=" CG ASN A 488 " pdb=" OD1 ASN A 488 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CG ASN B 960 " pdb=" OD1 ASN B 960 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.46e+01 bond pdb=" CD GLN B1436 " pdb=" OE1 GLN B1436 " ideal model delta sigma weight residual 1.231 1.322 -0.091 1.90e-02 2.77e+03 2.28e+01 ... (remaining 31435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 43144 2.21 - 4.41: 441 4.41 - 6.62: 62 6.62 - 8.83: 5 8.83 - 11.03: 2 Bond angle restraints: 43654 Sorted by residual: angle pdb=" C LEU B 869 " pdb=" CA LEU B 869 " pdb=" CB LEU B 869 " ideal model delta sigma weight residual 116.54 109.75 6.79 1.15e+00 7.56e-01 3.49e+01 angle pdb=" N ASP A 139 " pdb=" CA ASP A 139 " pdb=" C ASP A 139 " ideal model delta sigma weight residual 110.97 105.66 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N GLY B 868 " pdb=" CA GLY B 868 " pdb=" C GLY B 868 " ideal model delta sigma weight residual 113.18 124.21 -11.03 2.37e+00 1.78e-01 2.17e+01 angle pdb=" N ALA B 796 " pdb=" CA ALA B 796 " pdb=" C ALA B 796 " ideal model delta sigma weight residual 109.07 102.22 6.85 1.61e+00 3.86e-01 1.81e+01 angle pdb=" C3' U N 30 " pdb=" C2' U N 30 " pdb=" O2' U N 30 " ideal model delta sigma weight residual 110.70 116.93 -6.23 1.50e+00 4.44e-01 1.73e+01 ... (remaining 43649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 17990 35.98 - 71.96: 960 71.96 - 107.93: 73 107.93 - 143.91: 8 143.91 - 179.89: 6 Dihedral angle restraints: 19037 sinusoidal: 10417 harmonic: 8620 Sorted by residual: dihedral pdb=" O4' U N 85 " pdb=" C1' U N 85 " pdb=" N1 U N 85 " pdb=" C2 U N 85 " ideal model delta sinusoidal sigma weight residual 200.00 47.78 152.22 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" O4' U N 90 " pdb=" C1' U N 90 " pdb=" N1 U N 90 " pdb=" C2 U N 90 " ideal model delta sinusoidal sigma weight residual 232.00 52.11 179.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U N 101 " pdb=" C1' U N 101 " pdb=" N1 U N 101 " pdb=" C2 U N 101 " ideal model delta sinusoidal sigma weight residual -160.00 -40.03 -119.97 1 1.50e+01 4.44e-03 6.40e+01 ... (remaining 19034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4192 0.054 - 0.108: 655 0.108 - 0.162: 84 0.162 - 0.215: 4 0.215 - 0.269: 2 Chirality restraints: 4937 Sorted by residual: chirality pdb=" C2' U N 30 " pdb=" C3' U N 30 " pdb=" O2' U N 30 " pdb=" C1' U N 30 " both_signs ideal model delta sigma weight residual False -2.75 -2.48 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL B1348 " pdb=" CA VAL B1348 " pdb=" CG1 VAL B1348 " pdb=" CG2 VAL B1348 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' G O 107 " pdb=" C4' G O 107 " pdb=" O3' G O 107 " pdb=" C2' G O 107 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 4934 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N 36 " -0.036 2.00e-02 2.50e+03 1.82e-02 7.45e+00 pdb=" N1 C N 36 " 0.037 2.00e-02 2.50e+03 pdb=" C2 C N 36 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C N 36 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C N 36 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C N 36 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C N 36 " -0.012 2.00e-02 2.50e+03 pdb=" C5 C N 36 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C N 36 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 26 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C ASP G 26 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP G 26 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG G 27 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 326 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ARG A 326 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG A 326 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 327 " 0.014 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 290 2.56 - 3.14: 24262 3.14 - 3.73: 50904 3.73 - 4.31: 69446 4.31 - 4.90: 107988 Nonbonded interactions: 252890 Sorted by model distance: nonbonded pdb=" OD1 ASP G 9 " pdb="MG MG G 201 " model vdw 1.974 2.170 nonbonded pdb=" O ASN B1120 " pdb=" ND2 ASN B1120 " model vdw 2.068 3.120 nonbonded pdb=" O2 U N 35 " pdb=" N4 C N 36 " model vdw 2.156 3.120 nonbonded pdb=" O2' A N 11 " pdb=" O4' A N 12 " model vdw 2.174 3.040 nonbonded pdb=" O ILE H 82 " pdb=" OG SER H 86 " model vdw 2.197 3.040 ... (remaining 252885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'N' and resid 10 through 123) selection = chain 'O' } 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=0.46 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: 0.010 Normalize map: mean=0, sd=1: 4.130 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.470 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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 : 0.004 0.099 31440 Z= 0.185 Angle : 0.566 11.033 43654 Z= 0.315 Chirality : 0.040 0.269 4937 Planarity : 0.003 0.045 4540 Dihedral : 19.219 179.888 13451 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 0.33 % Allowed : 0.48 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.15), residues: 2913 helix: 1.12 (0.15), residues: 1169 sheet: -0.61 (0.27), residues: 347 loop : -0.86 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1252 TYR 0.016 0.001 TYR A 345 PHE 0.024 0.001 PHE A 140 TRP 0.020 0.001 TRP A 976 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00364 (31440) covalent geometry : angle 0.56621 (43654) hydrogen bonds : bond 0.13222 ( 1250) hydrogen bonds : angle 5.56352 ( 3290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 488 time to evaluate : 1.000 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: A 94 HIS cc_start: 0.7102 (p90) cc_final: 0.6777 (p90) REVERT: A 113 GLU cc_start: 0.7505 (tt0) cc_final: 0.7145 (tp30) REVERT: A 134 ASN cc_start: 0.8174 (m110) cc_final: 0.7923 (m110) REVERT: A 135 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7600 (tp30) REVERT: A 157 HIS cc_start: 0.6459 (t70) cc_final: 0.5955 (t70) REVERT: A 158 LEU cc_start: 0.6193 (mt) cc_final: 0.5854 (mt) REVERT: A 186 TYR cc_start: 0.7005 (t80) cc_final: 0.6233 (t80) REVERT: A 309 LYS cc_start: 0.7402 (pttp) cc_final: 0.7173 (ptpt) REVERT: A 317 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6782 (mp0) REVERT: A 334 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7581 (pt0) REVERT: A 335 PHE cc_start: 0.7958 (m-80) cc_final: 0.7468 (m-10) REVERT: A 680 ASN cc_start: 0.6752 (p0) cc_final: 0.6550 (p0) REVERT: A 706 LYS cc_start: 0.8057 (pttm) cc_final: 0.7646 (ptpp) REVERT: A 710 ASN cc_start: 0.7256 (m-40) cc_final: 0.6640 (m-40) REVERT: A 713 HIS cc_start: 0.6266 (m-70) cc_final: 0.6064 (m-70) REVERT: A 993 MET cc_start: 0.6669 (tpt) cc_final: 0.5676 (tpt) REVERT: A 995 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 1011 LYS cc_start: 0.8489 (ptpt) cc_final: 0.8194 (ptpt) REVERT: A 1113 ILE cc_start: 0.7880 (tp) cc_final: 0.7558 (tt) REVERT: A 1132 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6331 (mm-30) REVERT: A 1144 GLU cc_start: 0.7318 (pt0) cc_final: 0.7067 (pt0) REVERT: A 1172 TRP cc_start: 0.8108 (p-90) cc_final: 0.7199 (p-90) REVERT: A 1185 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7252 (mtp180) REVERT: A 1187 SER cc_start: 0.8085 (m) cc_final: 0.7719 (p) REVERT: A 1234 LYS cc_start: 0.7812 (pttp) cc_final: 0.7575 (pttm) REVERT: A 1250 LYS cc_start: 0.7855 (mttt) cc_final: 0.6991 (mtmt) REVERT: A 1302 GLU cc_start: 0.7671 (tt0) cc_final: 0.7288 (tt0) REVERT: A 1317 GLU cc_start: 0.6739 (tp30) cc_final: 0.6295 (tp30) REVERT: A 1323 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7737 (ttp80) REVERT: A 1389 THR cc_start: 0.8447 (m) cc_final: 0.8063 (m) REVERT: A 1436 GLN cc_start: 0.6322 (tp-100) cc_final: 0.5502 (tp-100) REVERT: B 103 LYS cc_start: 0.7383 (tptm) cc_final: 0.7069 (tptm) REVERT: B 133 PHE cc_start: 0.7739 (t80) cc_final: 0.7157 (t80) REVERT: B 161 LYS cc_start: 0.7967 (tttt) cc_final: 0.7640 (tttm) REVERT: B 168 GLU cc_start: 0.7660 (tp30) cc_final: 0.7083 (tt0) REVERT: B 169 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7408 (ptpt) REVERT: B 201 PHE cc_start: 0.7991 (t80) cc_final: 0.7513 (t80) REVERT: B 290 LYS cc_start: 0.7931 (mttp) cc_final: 0.7690 (mtmm) REVERT: B 306 GLN cc_start: 0.8350 (tp40) cc_final: 0.8039 (tp40) REVERT: B 324 GLU cc_start: 0.7913 (tt0) cc_final: 0.7658 (tt0) REVERT: B 326 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7324 (ttm110) REVERT: B 341 SER cc_start: 0.7431 (t) cc_final: 0.7100 (p) REVERT: B 373 MET cc_start: 0.8472 (ttp) cc_final: 0.8241 (ttp) REVERT: B 383 LEU cc_start: 0.7463 (mm) cc_final: 0.7232 (mp) REVERT: B 476 LYS cc_start: 0.8741 (mttm) cc_final: 0.8249 (mttm) REVERT: B 541 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6894 (tt0) REVERT: B 545 LYS cc_start: 0.6998 (mmtp) cc_final: 0.6741 (mmtt) REVERT: B 564 LYS cc_start: 0.8330 (mttt) cc_final: 0.7900 (mttt) REVERT: B 591 LYS cc_start: 0.8793 (tmmt) cc_final: 0.8493 (tmtt) REVERT: B 659 LYS cc_start: 0.8288 (tttt) cc_final: 0.7908 (tttp) REVERT: B 710 ASN cc_start: 0.7297 (m110) cc_final: 0.6842 (m110) REVERT: B 726 ASP cc_start: 0.7325 (m-30) cc_final: 0.6792 (m-30) REVERT: B 728 LYS cc_start: 0.7447 (pttm) cc_final: 0.6922 (pttt) REVERT: B 729 LYS cc_start: 0.7775 (ptmm) cc_final: 0.7536 (pttp) REVERT: B 733 GLN cc_start: 0.7203 (mp10) cc_final: 0.6957 (mp10) REVERT: B 745 LYS cc_start: 0.8553 (pttt) cc_final: 0.8333 (mmtp) REVERT: B 751 MET cc_start: 0.8018 (mmm) cc_final: 0.7702 (mmm) REVERT: B 869 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6047 (mm) REVERT: B 881 GLU cc_start: 0.8409 (tt0) cc_final: 0.7963 (tm-30) REVERT: B 923 MET cc_start: 0.6640 (tmm) cc_final: 0.6017 (tmm) REVERT: B 965 ASN cc_start: 0.6598 (p0) cc_final: 0.6303 (p0) REVERT: B 1022 LYS cc_start: 0.8175 (tttp) cc_final: 0.7778 (tptp) REVERT: B 1027 LYS cc_start: 0.6457 (mmmt) cc_final: 0.6055 (mmmt) REVERT: B 1107 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7885 (tttp) REVERT: B 1108 HIS cc_start: 0.6233 (m170) cc_final: 0.5921 (m170) REVERT: B 1116 SER cc_start: 0.8788 (t) cc_final: 0.8472 (p) REVERT: B 1130 TYR cc_start: 0.7037 (m-80) cc_final: 0.6640 (m-80) REVERT: B 1133 LYS cc_start: 0.6485 (ptmt) cc_final: 0.6223 (ttpp) REVERT: B 1147 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6577 (mm-30) REVERT: B 1211 ASN cc_start: 0.7086 (m-40) cc_final: 0.6707 (m-40) REVERT: B 1219 ASN cc_start: 0.7362 (t0) cc_final: 0.7150 (t0) REVERT: B 1255 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7257 (mm-30) REVERT: B 1323 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7029 (ttp-170) REVERT: B 1354 LYS cc_start: 0.7522 (ttpt) cc_final: 0.7165 (tptp) REVERT: B 1370 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6406 (mm-30) REVERT: B 1416 VAL cc_start: 0.8087 (m) cc_final: 0.7672 (p) REVERT: B 1423 LEU cc_start: 0.7943 (mt) cc_final: 0.7675 (mm) REVERT: B 1426 ILE cc_start: 0.8259 (mm) cc_final: 0.8017 (mp) REVERT: G 9 ASP cc_start: 0.6038 (t70) cc_final: 0.5827 (t70) REVERT: G 48 LYS cc_start: 0.7958 (mmmm) cc_final: 0.7756 (mmmm) REVERT: G 76 LEU cc_start: 0.8190 (mt) cc_final: 0.7968 (mm) REVERT: G 94 ASN cc_start: 0.7186 (t0) cc_final: 0.6914 (t0) REVERT: H 25 GLN cc_start: 0.7837 (tt0) cc_final: 0.7577 (tt0) REVERT: H 34 LYS cc_start: 0.7462 (mmmt) cc_final: 0.7240 (mmmt) REVERT: H 59 LYS cc_start: 0.7778 (mttp) cc_final: 0.7427 (tppp) REVERT: H 93 TYR cc_start: 0.8017 (m-80) cc_final: 0.5921 (m-80) REVERT: H 128 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7651 (mtmm) outliers start: 9 outliers final: 3 residues processed: 495 average time/residue: 0.2383 time to fit residues: 179.3953 Evaluate side-chains 427 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 423 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 1120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 50.0000 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 380 GLN A 551 HIS A1152 ASN B 944 ASN B 974 GLN G 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.218583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165366 restraints weight = 46978.047| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.81 r_work: 0.3678 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31440 Z= 0.195 Angle : 0.593 9.248 43654 Z= 0.318 Chirality : 0.042 0.213 4937 Planarity : 0.004 0.048 4540 Dihedral : 20.376 179.859 7097 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.18 % Allowed : 7.81 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.15), residues: 2913 helix: 1.07 (0.15), residues: 1192 sheet: -0.45 (0.27), residues: 346 loop : -0.88 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1028 TYR 0.024 0.002 TYR A 345 PHE 0.032 0.002 PHE B 871 TRP 0.018 0.002 TRP B1005 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00423 (31440) covalent geometry : angle 0.59280 (43654) hydrogen bonds : bond 0.04659 ( 1250) hydrogen bonds : angle 4.52557 ( 3290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 440 time to evaluate : 0.985 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: A 94 HIS cc_start: 0.7176 (p90) cc_final: 0.6889 (p90) REVERT: A 134 ASN cc_start: 0.7769 (m110) cc_final: 0.7516 (m110) REVERT: A 136 MET cc_start: 0.7033 (tmm) cc_final: 0.6759 (tmm) REVERT: A 186 TYR cc_start: 0.7064 (t80) cc_final: 0.6820 (t80) REVERT: A 317 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7255 (mp0) REVERT: A 333 LYS cc_start: 0.7707 (tttp) cc_final: 0.7501 (tptp) REVERT: A 667 GLU cc_start: 0.7378 (pp20) cc_final: 0.7147 (pp20) REVERT: A 696 ASP cc_start: 0.7999 (t0) cc_final: 0.7465 (t0) REVERT: A 708 PHE cc_start: 0.8321 (t80) cc_final: 0.8048 (t80) REVERT: A 710 ASN cc_start: 0.7818 (m-40) cc_final: 0.7365 (m-40) REVERT: A 993 MET cc_start: 0.6833 (tpt) cc_final: 0.5804 (tpt) REVERT: A 995 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 1011 LYS cc_start: 0.8474 (ptpt) cc_final: 0.8089 (ptpt) REVERT: A 1185 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7764 (mtp180) REVERT: A 1187 SER cc_start: 0.8356 (m) cc_final: 0.8139 (p) REVERT: A 1221 GLU cc_start: 0.8008 (mp0) cc_final: 0.7686 (mp0) REVERT: A 1239 TYR cc_start: 0.7889 (m-80) cc_final: 0.7666 (m-80) REVERT: A 1250 LYS cc_start: 0.7900 (mttt) cc_final: 0.7590 (mttt) REVERT: A 1302 GLU cc_start: 0.7586 (tt0) cc_final: 0.7367 (tt0) REVERT: A 1305 GLU cc_start: 0.7681 (tp30) cc_final: 0.7236 (tm-30) REVERT: A 1317 GLU cc_start: 0.7137 (tp30) cc_final: 0.6905 (tp30) REVERT: A 1383 LYS cc_start: 0.8113 (tttm) cc_final: 0.7811 (tttt) REVERT: A 1436 GLN cc_start: 0.6135 (tp-100) cc_final: 0.5573 (tp-100) REVERT: B 168 GLU cc_start: 0.7796 (tp30) cc_final: 0.7253 (tt0) REVERT: B 169 LYS cc_start: 0.7947 (ptpt) cc_final: 0.7700 (ptpt) REVERT: B 192 ASP cc_start: 0.0580 (OUTLIER) cc_final: 0.0354 (p0) REVERT: B 201 PHE cc_start: 0.8006 (t80) cc_final: 0.7797 (t80) REVERT: B 282 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 298 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: B 306 GLN cc_start: 0.8326 (tp40) cc_final: 0.8093 (tp40) REVERT: B 383 LEU cc_start: 0.7992 (mm) cc_final: 0.7585 (mp) REVERT: B 476 LYS cc_start: 0.8666 (mttm) cc_final: 0.8268 (mttm) REVERT: B 564 LYS cc_start: 0.8780 (mttt) cc_final: 0.8375 (mttt) REVERT: B 726 ASP cc_start: 0.7114 (m-30) cc_final: 0.6814 (m-30) REVERT: B 728 LYS cc_start: 0.7623 (pttm) cc_final: 0.7327 (pmtt) REVERT: B 751 MET cc_start: 0.7847 (mmm) cc_final: 0.7419 (mmm) REVERT: B 881 GLU cc_start: 0.7577 (tt0) cc_final: 0.7221 (tm-30) REVERT: B 923 MET cc_start: 0.6344 (tmm) cc_final: 0.5625 (tmm) REVERT: B 1000 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7560 (mmtm) REVERT: B 1027 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6617 (mmtt) REVERT: B 1107 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8329 (tttp) REVERT: B 1108 HIS cc_start: 0.6461 (m170) cc_final: 0.6243 (m170) REVERT: B 1120 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7199 (p0) REVERT: B 1147 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 1211 ASN cc_start: 0.7316 (m-40) cc_final: 0.6968 (m-40) REVERT: B 1219 ASN cc_start: 0.7690 (t0) cc_final: 0.7437 (t0) REVERT: B 1255 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 1305 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 1323 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7773 (ptt180) REVERT: B 1416 VAL cc_start: 0.8507 (m) cc_final: 0.8204 (p) REVERT: B 1426 ILE cc_start: 0.8268 (mm) cc_final: 0.8059 (mp) REVERT: B 1427 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6995 (t0) REVERT: G 13 LEU cc_start: 0.8230 (mm) cc_final: 0.7908 (mp) REVERT: G 30 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6672 (pm20) REVERT: G 48 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8307 (mmmm) REVERT: G 52 ARG cc_start: 0.6338 (tpp80) cc_final: 0.6128 (tpp80) REVERT: H 25 GLN cc_start: 0.8054 (tt0) cc_final: 0.7830 (tt0) REVERT: H 126 ASP cc_start: 0.8586 (t0) cc_final: 0.8005 (t70) REVERT: H 128 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8093 (mtmm) outliers start: 32 outliers final: 19 residues processed: 452 average time/residue: 0.2415 time to fit residues: 166.0976 Evaluate side-chains 435 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 411 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 265 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A1152 ASN G 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.218857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165197 restraints weight = 46845.284| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.74 r_work: 0.3685 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.167 Angle : 0.559 9.201 43654 Z= 0.301 Chirality : 0.041 0.217 4937 Planarity : 0.003 0.044 4540 Dihedral : 20.286 179.858 7092 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 1.85 % Allowed : 10.70 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.15), residues: 2913 helix: 1.14 (0.15), residues: 1190 sheet: -0.35 (0.27), residues: 349 loop : -0.89 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 80 TYR 0.030 0.001 TYR B1064 PHE 0.024 0.001 PHE B1073 TRP 0.025 0.001 TRP B1005 HIS 0.008 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00364 (31440) covalent geometry : angle 0.55903 (43654) hydrogen bonds : bond 0.04227 ( 1250) hydrogen bonds : angle 4.26879 ( 3290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 1.035 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: A 134 ASN cc_start: 0.7791 (m110) cc_final: 0.7488 (m110) REVERT: A 136 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6781 (tmm) REVERT: A 186 TYR cc_start: 0.7067 (t80) cc_final: 0.6726 (t80) REVERT: A 317 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 334 GLU cc_start: 0.7455 (pt0) cc_final: 0.7206 (pm20) REVERT: A 338 GLU cc_start: 0.7602 (mp0) cc_final: 0.7389 (mp0) REVERT: A 366 LYS cc_start: 0.7245 (mmmt) cc_final: 0.6153 (mppt) REVERT: A 667 GLU cc_start: 0.7423 (pp20) cc_final: 0.7120 (pp20) REVERT: A 696 ASP cc_start: 0.8001 (t0) cc_final: 0.7496 (t0) REVERT: A 708 PHE cc_start: 0.8250 (t80) cc_final: 0.8041 (t80) REVERT: A 710 ASN cc_start: 0.7751 (m-40) cc_final: 0.7308 (m110) REVERT: A 936 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7486 (pttt) REVERT: A 993 MET cc_start: 0.6838 (tpt) cc_final: 0.5812 (tpt) REVERT: A 995 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 1011 LYS cc_start: 0.8469 (ptpt) cc_final: 0.8032 (ptpt) REVERT: A 1099 TRP cc_start: 0.6711 (p90) cc_final: 0.6148 (p90) REVERT: A 1102 PHE cc_start: 0.7431 (t80) cc_final: 0.7158 (t80) REVERT: A 1185 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7738 (mtp180) REVERT: A 1187 SER cc_start: 0.8384 (m) cc_final: 0.8162 (p) REVERT: A 1250 LYS cc_start: 0.7852 (mttt) cc_final: 0.7557 (mttt) REVERT: A 1305 GLU cc_start: 0.7664 (tp30) cc_final: 0.7441 (tp30) REVERT: A 1309 GLN cc_start: 0.7853 (mm110) cc_final: 0.7579 (mm-40) REVERT: A 1325 LEU cc_start: 0.8138 (mm) cc_final: 0.7936 (mp) REVERT: A 1382 ILE cc_start: 0.8308 (mt) cc_final: 0.8041 (mt) REVERT: A 1383 LYS cc_start: 0.8042 (tttm) cc_final: 0.7792 (tttt) REVERT: A 1436 GLN cc_start: 0.6087 (tp-100) cc_final: 0.5562 (tp-100) REVERT: B 102 GLU cc_start: 0.7253 (mp0) cc_final: 0.6903 (pm20) REVERT: B 168 GLU cc_start: 0.7763 (tp30) cc_final: 0.7290 (tt0) REVERT: B 290 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7627 (mtmm) REVERT: B 298 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: B 306 GLN cc_start: 0.8337 (tp40) cc_final: 0.8107 (tp40) REVERT: B 309 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8146 (mmmm) REVERT: B 347 ASP cc_start: 0.6487 (m-30) cc_final: 0.6093 (m-30) REVERT: B 383 LEU cc_start: 0.7970 (mm) cc_final: 0.7589 (mp) REVERT: B 425 PHE cc_start: 0.6866 (m-10) cc_final: 0.6506 (m-10) REVERT: B 476 LYS cc_start: 0.8610 (mttm) cc_final: 0.8203 (mttm) REVERT: B 545 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7729 (mmtt) REVERT: B 564 LYS cc_start: 0.8808 (mttt) cc_final: 0.8407 (mttt) REVERT: B 587 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.4528 (mtt) REVERT: B 593 TRP cc_start: 0.5672 (t60) cc_final: 0.5365 (t60) REVERT: B 726 ASP cc_start: 0.7116 (m-30) cc_final: 0.6803 (m-30) REVERT: B 728 LYS cc_start: 0.7655 (pttm) cc_final: 0.7423 (pmtt) REVERT: B 733 GLN cc_start: 0.7713 (mp10) cc_final: 0.7458 (mp10) REVERT: B 751 MET cc_start: 0.7917 (mmm) cc_final: 0.7420 (mmm) REVERT: B 865 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.6426 (p0) REVERT: B 1000 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7517 (mmtm) REVERT: B 1027 LYS cc_start: 0.6912 (mmmt) cc_final: 0.6527 (mmtt) REVERT: B 1064 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 1107 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8254 (tttp) REVERT: B 1108 HIS cc_start: 0.6495 (m170) cc_final: 0.6251 (m170) REVERT: B 1120 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7095 (p0) REVERT: B 1133 LYS cc_start: 0.6901 (ttpp) cc_final: 0.6514 (tttp) REVERT: B 1188 LEU cc_start: 0.8570 (tp) cc_final: 0.8347 (mt) REVERT: B 1211 ASN cc_start: 0.7316 (m-40) cc_final: 0.6969 (m-40) REVERT: B 1219 ASN cc_start: 0.7855 (t0) cc_final: 0.7537 (t0) REVERT: B 1255 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 1305 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 1323 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7697 (ptt180) REVERT: B 1377 ASP cc_start: 0.7151 (p0) cc_final: 0.6627 (t0) REVERT: B 1416 VAL cc_start: 0.8494 (m) cc_final: 0.8207 (p) REVERT: B 1427 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.7038 (t0) REVERT: G 13 LEU cc_start: 0.8278 (mm) cc_final: 0.7938 (mp) REVERT: G 30 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: G 48 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8294 (mmmm) REVERT: G 130 LYS cc_start: 0.7516 (ttmm) cc_final: 0.7284 (ttmm) REVERT: H 25 GLN cc_start: 0.8037 (tt0) cc_final: 0.7753 (tt0) REVERT: H 62 THR cc_start: 0.8469 (m) cc_final: 0.8231 (t) REVERT: H 119 MET cc_start: 0.7562 (mmm) cc_final: 0.7195 (mtp) REVERT: H 126 ASP cc_start: 0.8565 (t0) cc_final: 0.7913 (t70) REVERT: H 128 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8119 (mtmm) outliers start: 50 outliers final: 22 residues processed: 445 average time/residue: 0.2461 time to fit residues: 166.7663 Evaluate side-chains 437 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 406 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 67 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 151 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 246 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 651 HIS A 685 GLN A1152 ASN B 675 GLN B 710 ASN B 739 ASN B 960 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.217713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164775 restraints weight = 46350.322| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.81 r_work: 0.3662 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.204 Angle : 0.574 9.884 43654 Z= 0.309 Chirality : 0.042 0.213 4937 Planarity : 0.004 0.043 4540 Dihedral : 20.273 179.098 7092 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 2.04 % Allowed : 12.58 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.15), residues: 2913 helix: 1.01 (0.15), residues: 1196 sheet: -0.39 (0.27), residues: 353 loop : -0.94 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 80 TYR 0.021 0.001 TYR A 297 PHE 0.024 0.002 PHE G 88 TRP 0.031 0.002 TRP B1005 HIS 0.008 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00445 (31440) covalent geometry : angle 0.57376 (43654) hydrogen bonds : bond 0.04460 ( 1250) hydrogen bonds : angle 4.22810 ( 3290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 421 time to evaluate : 0.833 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: A 94 HIS cc_start: 0.6876 (p90) cc_final: 0.6651 (p90) REVERT: A 134 ASN cc_start: 0.7797 (m110) cc_final: 0.7481 (m110) REVERT: A 297 TYR cc_start: 0.5027 (t80) cc_final: 0.4549 (t80) REVERT: A 328 ILE cc_start: 0.7320 (pt) cc_final: 0.7027 (mt) REVERT: A 667 GLU cc_start: 0.7465 (pp20) cc_final: 0.7161 (pp20) REVERT: A 696 ASP cc_start: 0.8083 (t0) cc_final: 0.7558 (t0) REVERT: A 993 MET cc_start: 0.6876 (tpt) cc_final: 0.5798 (tpt) REVERT: A 995 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 1011 LYS cc_start: 0.8496 (ptpt) cc_final: 0.8064 (ptpt) REVERT: A 1099 TRP cc_start: 0.6740 (p90) cc_final: 0.6200 (p90) REVERT: A 1172 TRP cc_start: 0.8206 (p90) cc_final: 0.7790 (p90) REVERT: A 1185 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7696 (mtp180) REVERT: A 1250 LYS cc_start: 0.7834 (mttt) cc_final: 0.7473 (mttt) REVERT: A 1305 GLU cc_start: 0.7655 (tp30) cc_final: 0.7185 (tm-30) REVERT: A 1325 LEU cc_start: 0.8108 (mm) cc_final: 0.7877 (mp) REVERT: A 1356 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7561 (mtpp) REVERT: A 1376 GLN cc_start: 0.8019 (pp30) cc_final: 0.7648 (pp30) REVERT: A 1383 LYS cc_start: 0.8072 (tttm) cc_final: 0.7863 (tttt) REVERT: A 1410 ARG cc_start: 0.5432 (ttt90) cc_final: 0.5144 (ttt90) REVERT: A 1436 GLN cc_start: 0.6076 (tp-100) cc_final: 0.5646 (tp-100) REVERT: B 168 GLU cc_start: 0.7754 (tp30) cc_final: 0.7287 (tt0) REVERT: B 169 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7696 (ptpt) REVERT: B 201 PHE cc_start: 0.8130 (t80) cc_final: 0.7789 (t80) REVERT: B 290 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7656 (mtmm) REVERT: B 306 GLN cc_start: 0.8351 (tp40) cc_final: 0.8133 (tp40) REVERT: B 313 VAL cc_start: 0.8668 (t) cc_final: 0.8391 (p) REVERT: B 347 ASP cc_start: 0.6468 (m-30) cc_final: 0.6113 (m-30) REVERT: B 383 LEU cc_start: 0.7976 (mm) cc_final: 0.7642 (mp) REVERT: B 432 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7241 (t80) REVERT: B 476 LYS cc_start: 0.8586 (mttm) cc_final: 0.8193 (mttm) REVERT: B 545 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7856 (mptt) REVERT: B 564 LYS cc_start: 0.8880 (mttt) cc_final: 0.8494 (mttt) REVERT: B 593 TRP cc_start: 0.6039 (t60) cc_final: 0.5836 (t60) REVERT: B 678 LEU cc_start: 0.8885 (mm) cc_final: 0.8677 (mp) REVERT: B 726 ASP cc_start: 0.7106 (m-30) cc_final: 0.6766 (m-30) REVERT: B 728 LYS cc_start: 0.7839 (pttm) cc_final: 0.7568 (pttt) REVERT: B 733 GLN cc_start: 0.7813 (mp10) cc_final: 0.7540 (mp10) REVERT: B 751 MET cc_start: 0.7963 (mmm) cc_final: 0.7379 (mmm) REVERT: B 865 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6553 (p0) REVERT: B 881 GLU cc_start: 0.7664 (tt0) cc_final: 0.7351 (tm-30) REVERT: B 995 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 1000 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7530 (mmtm) REVERT: B 1027 LYS cc_start: 0.7108 (mmmt) cc_final: 0.6594 (mmtt) REVERT: B 1064 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.7143 (t80) REVERT: B 1067 LYS cc_start: 0.8889 (pptt) cc_final: 0.8672 (pptt) REVERT: B 1107 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8259 (tttp) REVERT: B 1108 HIS cc_start: 0.6602 (m170) cc_final: 0.6399 (m170) REVERT: B 1120 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7230 (p0) REVERT: B 1143 LYS cc_start: 0.6978 (mttm) cc_final: 0.6493 (mttm) REVERT: B 1147 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7242 (mm-30) REVERT: B 1255 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 1305 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 1323 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7682 (ptt180) REVERT: B 1416 VAL cc_start: 0.8510 (m) cc_final: 0.8191 (p) REVERT: G 6 ILE cc_start: 0.7878 (mm) cc_final: 0.7495 (tt) REVERT: G 13 LEU cc_start: 0.8294 (mm) cc_final: 0.8056 (mp) REVERT: G 30 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: G 48 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8282 (mmmm) REVERT: G 76 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8159 (mt) REVERT: G 123 MET cc_start: 0.7868 (tmm) cc_final: 0.6840 (ptm) REVERT: G 130 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7367 (ttmm) REVERT: H 18 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: H 25 GLN cc_start: 0.8106 (tt0) cc_final: 0.7805 (tt0) REVERT: H 93 TYR cc_start: 0.8203 (m-80) cc_final: 0.6599 (m-80) REVERT: H 128 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8104 (mtmm) outliers start: 55 outliers final: 34 residues processed: 446 average time/residue: 0.2224 time to fit residues: 152.1177 Evaluate side-chains 445 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 404 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 685 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 27 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 28 optimal weight: 30.0000 chunk 48 optimal weight: 0.4980 chunk 131 optimal weight: 0.4980 chunk 147 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS A1152 ASN B 477 HIS B 710 ASN B 739 ASN B 960 ASN B 979 ASN B1427 ASN G 109 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.217110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163614 restraints weight = 46545.987| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.73 r_work: 0.3656 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31440 Z= 0.211 Angle : 0.575 9.733 43654 Z= 0.310 Chirality : 0.042 0.209 4937 Planarity : 0.004 0.042 4540 Dihedral : 20.250 178.742 7092 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 13.32 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.15), residues: 2913 helix: 0.95 (0.15), residues: 1203 sheet: -0.39 (0.27), residues: 353 loop : -0.93 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.032 0.001 TYR A 379 PHE 0.021 0.002 PHE A 709 TRP 0.033 0.002 TRP B1005 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00463 (31440) covalent geometry : angle 0.57486 (43654) hydrogen bonds : bond 0.04455 ( 1250) hydrogen bonds : angle 4.23921 ( 3290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 418 time to evaluate : 0.850 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: A 13 ASN cc_start: 0.8328 (p0) cc_final: 0.7880 (p0) REVERT: A 94 HIS cc_start: 0.6995 (p90) cc_final: 0.6793 (p90) REVERT: A 134 ASN cc_start: 0.7763 (m110) cc_final: 0.7452 (m110) REVERT: A 136 MET cc_start: 0.7078 (tmm) cc_final: 0.6749 (tmm) REVERT: A 171 GLU cc_start: 0.7091 (mm-30) cc_final: 0.5425 (mt-10) REVERT: A 297 TYR cc_start: 0.5214 (t80) cc_final: 0.4803 (t80) REVERT: A 303 ASN cc_start: 0.7221 (t0) cc_final: 0.6434 (p0) REVERT: A 309 LYS cc_start: 0.7662 (pttp) cc_final: 0.7400 (ptmt) REVERT: A 317 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 328 ILE cc_start: 0.7357 (pt) cc_final: 0.7114 (mt) REVERT: A 333 LYS cc_start: 0.8105 (tptm) cc_final: 0.7738 (tppt) REVERT: A 379 TYR cc_start: 0.6970 (t80) cc_final: 0.6764 (t80) REVERT: A 667 GLU cc_start: 0.7509 (pp20) cc_final: 0.7167 (pp20) REVERT: A 696 ASP cc_start: 0.8048 (t0) cc_final: 0.7548 (t0) REVERT: A 993 MET cc_start: 0.6882 (tpt) cc_final: 0.5821 (tpt) REVERT: A 995 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 1011 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8086 (ptpt) REVERT: A 1099 TRP cc_start: 0.6732 (p90) cc_final: 0.6261 (p90) REVERT: A 1172 TRP cc_start: 0.8246 (p90) cc_final: 0.7789 (p90) REVERT: A 1185 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7737 (mtp180) REVERT: A 1211 ASN cc_start: 0.7426 (m110) cc_final: 0.6891 (m110) REVERT: A 1250 LYS cc_start: 0.7908 (mttt) cc_final: 0.7533 (mtmt) REVERT: A 1305 GLU cc_start: 0.7664 (tp30) cc_final: 0.7235 (tm-30) REVERT: A 1325 LEU cc_start: 0.8141 (mm) cc_final: 0.7892 (mp) REVERT: A 1356 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7563 (mtpp) REVERT: A 1376 GLN cc_start: 0.8068 (pp30) cc_final: 0.7635 (pp30) REVERT: A 1383 LYS cc_start: 0.8053 (tttm) cc_final: 0.7833 (tttt) REVERT: A 1410 ARG cc_start: 0.5454 (ttt90) cc_final: 0.5174 (ttt90) REVERT: A 1436 GLN cc_start: 0.6068 (tp-100) cc_final: 0.5643 (tp-100) REVERT: B 168 GLU cc_start: 0.7764 (tp30) cc_final: 0.7334 (tt0) REVERT: B 169 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7685 (ptpt) REVERT: B 201 PHE cc_start: 0.8010 (t80) cc_final: 0.7711 (t80) REVERT: B 313 VAL cc_start: 0.8676 (t) cc_final: 0.8417 (p) REVERT: B 365 LYS cc_start: 0.7314 (mmpt) cc_final: 0.7096 (mmpt) REVERT: B 383 LEU cc_start: 0.7986 (mm) cc_final: 0.7632 (mp) REVERT: B 425 PHE cc_start: 0.6828 (m-10) cc_final: 0.6606 (m-10) REVERT: B 432 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7205 (t80) REVERT: B 476 LYS cc_start: 0.8597 (mttm) cc_final: 0.8211 (mttm) REVERT: B 499 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 545 LYS cc_start: 0.8069 (mmtp) cc_final: 0.7863 (mptt) REVERT: B 564 LYS cc_start: 0.8883 (mttt) cc_final: 0.8498 (mttt) REVERT: B 587 MET cc_start: 0.5592 (mtt) cc_final: 0.5089 (mtt) REVERT: B 726 ASP cc_start: 0.7137 (m-30) cc_final: 0.6779 (m-30) REVERT: B 728 LYS cc_start: 0.7948 (pttm) cc_final: 0.7723 (pttt) REVERT: B 733 GLN cc_start: 0.7865 (mp10) cc_final: 0.7579 (mp10) REVERT: B 751 MET cc_start: 0.7957 (mmm) cc_final: 0.7271 (mmm) REVERT: B 817 PRO cc_start: 0.7390 (Cg_exo) cc_final: 0.7189 (Cg_endo) REVERT: B 865 ASN cc_start: 0.6767 (OUTLIER) cc_final: 0.6503 (p0) REVERT: B 881 GLU cc_start: 0.7647 (tt0) cc_final: 0.7348 (tm-30) REVERT: B 995 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 1000 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7689 (mmtm) REVERT: B 1027 LYS cc_start: 0.7184 (mmmt) cc_final: 0.6867 (mmtt) REVERT: B 1067 LYS cc_start: 0.8856 (pptt) cc_final: 0.8553 (pptt) REVERT: B 1107 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8286 (tttp) REVERT: B 1108 HIS cc_start: 0.6692 (m170) cc_final: 0.6481 (m170) REVERT: B 1120 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7205 (p0) REVERT: B 1135 VAL cc_start: 0.7506 (m) cc_final: 0.7279 (t) REVERT: B 1143 LYS cc_start: 0.6965 (mttm) cc_final: 0.6460 (mttm) REVERT: B 1147 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7262 (mm-30) REVERT: B 1255 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 1305 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 1323 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7656 (ptt180) REVERT: B 1416 VAL cc_start: 0.8476 (m) cc_final: 0.8159 (p) REVERT: G 6 ILE cc_start: 0.7972 (mm) cc_final: 0.7571 (tt) REVERT: G 13 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8035 (mp) REVERT: G 30 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: G 87 GLN cc_start: 0.8162 (tt0) cc_final: 0.7942 (tt0) REVERT: G 130 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7362 (ttmm) REVERT: H 18 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: H 25 GLN cc_start: 0.8089 (tt0) cc_final: 0.7767 (tt0) REVERT: H 93 TYR cc_start: 0.8213 (m-80) cc_final: 0.6514 (m-80) REVERT: H 126 ASP cc_start: 0.8546 (t0) cc_final: 0.7994 (t70) REVERT: H 128 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8125 (mtmm) outliers start: 62 outliers final: 46 residues processed: 445 average time/residue: 0.1951 time to fit residues: 133.1398 Evaluate side-chains 460 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 64 optimal weight: 30.0000 chunk 217 optimal weight: 0.6980 chunk 227 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 260 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 167 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 98 GLN B 710 ASN B 960 ASN B1427 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.217911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164463 restraints weight = 46521.358| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.76 r_work: 0.3669 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.180 Angle : 0.559 9.677 43654 Z= 0.301 Chirality : 0.041 0.202 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.212 178.446 7092 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 2.33 % Allowed : 14.17 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.15), residues: 2913 helix: 1.04 (0.15), residues: 1193 sheet: -0.34 (0.27), residues: 353 loop : -0.92 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.025 0.001 TYR A 379 PHE 0.018 0.001 PHE B 462 TRP 0.037 0.002 TRP B1005 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00394 (31440) covalent geometry : angle 0.55871 (43654) hydrogen bonds : bond 0.04208 ( 1250) hydrogen bonds : angle 4.16788 ( 3290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 0.781 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: A 13 ASN cc_start: 0.8333 (p0) cc_final: 0.7890 (p0) REVERT: A 34 MET cc_start: 0.6736 (mmm) cc_final: 0.6290 (mmt) REVERT: A 94 HIS cc_start: 0.7035 (p90) cc_final: 0.6814 (p90) REVERT: A 107 LYS cc_start: 0.8305 (mttt) cc_final: 0.8081 (mttp) REVERT: A 134 ASN cc_start: 0.7756 (m110) cc_final: 0.7442 (m110) REVERT: A 171 GLU cc_start: 0.7072 (mm-30) cc_final: 0.5273 (mt-10) REVERT: A 181 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7186 (m-70) REVERT: A 297 TYR cc_start: 0.5112 (t80) cc_final: 0.4698 (t80) REVERT: A 303 ASN cc_start: 0.7276 (t0) cc_final: 0.6483 (p0) REVERT: A 309 LYS cc_start: 0.7629 (pttp) cc_final: 0.7321 (ptpt) REVERT: A 317 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 328 ILE cc_start: 0.7300 (pt) cc_final: 0.7051 (mt) REVERT: A 333 LYS cc_start: 0.8007 (tptm) cc_final: 0.7629 (tppt) REVERT: A 379 TYR cc_start: 0.7011 (t80) cc_final: 0.6721 (t80) REVERT: A 667 GLU cc_start: 0.7533 (pp20) cc_final: 0.7178 (pp20) REVERT: A 696 ASP cc_start: 0.8010 (t0) cc_final: 0.7504 (t0) REVERT: A 993 MET cc_start: 0.6844 (tpt) cc_final: 0.5794 (tpt) REVERT: A 995 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7283 (tm-30) REVERT: A 1011 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8059 (ptpt) REVERT: A 1099 TRP cc_start: 0.6714 (p90) cc_final: 0.6328 (p90) REVERT: A 1185 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7741 (mtp180) REVERT: A 1211 ASN cc_start: 0.7454 (m110) cc_final: 0.6913 (m110) REVERT: A 1250 LYS cc_start: 0.7898 (mttt) cc_final: 0.7524 (mtmt) REVERT: A 1305 GLU cc_start: 0.7646 (tp30) cc_final: 0.7220 (tm-30) REVERT: A 1325 LEU cc_start: 0.8138 (mm) cc_final: 0.7879 (mp) REVERT: A 1356 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7580 (mtpp) REVERT: A 1376 GLN cc_start: 0.8066 (pp30) cc_final: 0.7523 (pp30) REVERT: A 1388 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7739 (ttpp) REVERT: A 1436 GLN cc_start: 0.6112 (tp-100) cc_final: 0.5712 (tp-100) REVERT: B 90 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 168 GLU cc_start: 0.7750 (tp30) cc_final: 0.7278 (tt0) REVERT: B 201 PHE cc_start: 0.7944 (t80) cc_final: 0.7667 (t80) REVERT: B 290 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7800 (mmmt) REVERT: B 313 VAL cc_start: 0.8676 (t) cc_final: 0.8423 (p) REVERT: B 338 GLU cc_start: 0.7262 (mp0) cc_final: 0.6522 (mt-10) REVERT: B 365 LYS cc_start: 0.7314 (mmpt) cc_final: 0.7104 (mmpt) REVERT: B 383 LEU cc_start: 0.7968 (mm) cc_final: 0.7611 (mp) REVERT: B 425 PHE cc_start: 0.6865 (m-10) cc_final: 0.6645 (m-10) REVERT: B 432 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 476 LYS cc_start: 0.8648 (mttm) cc_final: 0.8273 (mttm) REVERT: B 499 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7326 (mm-30) REVERT: B 545 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7854 (mptt) REVERT: B 564 LYS cc_start: 0.8873 (mttt) cc_final: 0.8483 (mttt) REVERT: B 587 MET cc_start: 0.5641 (mtt) cc_final: 0.5119 (mtt) REVERT: B 726 ASP cc_start: 0.7155 (m-30) cc_final: 0.6809 (m-30) REVERT: B 733 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7588 (mp10) REVERT: B 751 MET cc_start: 0.7967 (mmm) cc_final: 0.7290 (mmm) REVERT: B 817 PRO cc_start: 0.7538 (Cg_exo) cc_final: 0.7331 (Cg_endo) REVERT: B 865 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6496 (p0) REVERT: B 881 GLU cc_start: 0.7589 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 995 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 1000 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7586 (mmtm) REVERT: B 1027 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6771 (mmtt) REVERT: B 1067 LYS cc_start: 0.8816 (pptt) cc_final: 0.8486 (pptt) REVERT: B 1107 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8174 (tttp) REVERT: B 1108 HIS cc_start: 0.6674 (m170) cc_final: 0.6453 (m170) REVERT: B 1120 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7141 (p0) REVERT: B 1135 VAL cc_start: 0.7438 (m) cc_final: 0.7224 (t) REVERT: B 1143 LYS cc_start: 0.6970 (mttm) cc_final: 0.6444 (mttm) REVERT: B 1147 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7249 (mm-30) REVERT: B 1255 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 1305 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 1323 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7624 (ptt180) REVERT: B 1416 VAL cc_start: 0.8506 (m) cc_final: 0.8175 (p) REVERT: G 6 ILE cc_start: 0.7999 (mm) cc_final: 0.7582 (tt) REVERT: G 13 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8033 (mp) REVERT: G 30 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: G 87 GLN cc_start: 0.8151 (tt0) cc_final: 0.7935 (tt0) REVERT: G 123 MET cc_start: 0.7815 (tmm) cc_final: 0.6507 (ptm) REVERT: G 130 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7366 (ttmm) REVERT: H 18 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: H 25 GLN cc_start: 0.8037 (tt0) cc_final: 0.7689 (tt0) REVERT: H 93 TYR cc_start: 0.8193 (m-80) cc_final: 0.6459 (m-10) REVERT: H 126 ASP cc_start: 0.8540 (t0) cc_final: 0.7969 (t70) REVERT: H 128 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8145 (mtmm) outliers start: 63 outliers final: 45 residues processed: 435 average time/residue: 0.1828 time to fit residues: 121.8807 Evaluate side-chains 452 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 398 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 61 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 192 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 132 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 98 GLN B 306 GLN B 477 HIS B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN B 974 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.217921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.164358 restraints weight = 46587.815| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.78 r_work: 0.3663 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.180 Angle : 0.552 9.197 43654 Z= 0.298 Chirality : 0.040 0.194 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.182 177.962 7092 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 2.52 % Allowed : 14.73 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.15), residues: 2913 helix: 1.02 (0.15), residues: 1204 sheet: -0.31 (0.27), residues: 352 loop : -0.94 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 104 TYR 0.025 0.001 TYR A 379 PHE 0.028 0.001 PHE G 88 TRP 0.044 0.002 TRP B1005 HIS 0.007 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00393 (31440) covalent geometry : angle 0.55221 (43654) hydrogen bonds : bond 0.04186 ( 1250) hydrogen bonds : angle 4.12377 ( 3290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 409 time to evaluate : 0.852 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: A 13 ASN cc_start: 0.8334 (p0) cc_final: 0.7889 (p0) REVERT: A 34 MET cc_start: 0.6775 (mmm) cc_final: 0.6456 (mmt) REVERT: A 94 HIS cc_start: 0.7043 (p90) cc_final: 0.6805 (p90) REVERT: A 107 LYS cc_start: 0.8303 (mttt) cc_final: 0.8068 (mttp) REVERT: A 136 MET cc_start: 0.6984 (tmm) cc_final: 0.6730 (tmm) REVERT: A 181 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7247 (m-70) REVERT: A 297 TYR cc_start: 0.5139 (t80) cc_final: 0.4741 (t80) REVERT: A 303 ASN cc_start: 0.7228 (t0) cc_final: 0.6501 (p0) REVERT: A 309 LYS cc_start: 0.7582 (pttp) cc_final: 0.7273 (ptpt) REVERT: A 317 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7083 (mm-30) REVERT: A 328 ILE cc_start: 0.7295 (pt) cc_final: 0.7031 (mt) REVERT: A 379 TYR cc_start: 0.7132 (t80) cc_final: 0.6679 (t80) REVERT: A 667 GLU cc_start: 0.7545 (pp20) cc_final: 0.7306 (pp20) REVERT: A 688 THR cc_start: 0.7648 (m) cc_final: 0.7390 (p) REVERT: A 993 MET cc_start: 0.6840 (tpt) cc_final: 0.5780 (tpt) REVERT: A 995 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 1011 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8099 (ptpt) REVERT: A 1037 ASP cc_start: 0.7198 (m-30) cc_final: 0.6974 (m-30) REVERT: A 1099 TRP cc_start: 0.6758 (p90) cc_final: 0.6397 (p90) REVERT: A 1185 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7717 (mtp180) REVERT: A 1211 ASN cc_start: 0.7473 (m110) cc_final: 0.6947 (m110) REVERT: A 1250 LYS cc_start: 0.7898 (mttt) cc_final: 0.7459 (mtmt) REVERT: A 1325 LEU cc_start: 0.8161 (mm) cc_final: 0.7883 (mp) REVERT: A 1356 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7564 (mtpp) REVERT: A 1376 GLN cc_start: 0.8088 (pp30) cc_final: 0.7533 (pp30) REVERT: A 1388 LYS cc_start: 0.7984 (tmtt) cc_final: 0.7691 (ttpp) REVERT: A 1436 GLN cc_start: 0.6124 (tp-100) cc_final: 0.5723 (tp-100) REVERT: B 90 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 102 GLU cc_start: 0.7272 (mp0) cc_final: 0.6824 (pm20) REVERT: B 168 GLU cc_start: 0.7731 (tp30) cc_final: 0.7244 (tt0) REVERT: B 201 PHE cc_start: 0.7931 (t80) cc_final: 0.7720 (t80) REVERT: B 298 GLU cc_start: 0.6414 (mp0) cc_final: 0.5912 (mp0) REVERT: B 315 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (t) REVERT: B 338 GLU cc_start: 0.7244 (mp0) cc_final: 0.6541 (mt-10) REVERT: B 340 GLN cc_start: 0.6996 (mt0) cc_final: 0.6753 (mt0) REVERT: B 365 LYS cc_start: 0.7308 (mmpt) cc_final: 0.7082 (mmpt) REVERT: B 383 LEU cc_start: 0.7984 (mm) cc_final: 0.7635 (mp) REVERT: B 425 PHE cc_start: 0.6867 (m-10) cc_final: 0.6653 (m-10) REVERT: B 429 GLN cc_start: 0.8005 (mm-40) cc_final: 0.6824 (mm-40) REVERT: B 432 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 476 LYS cc_start: 0.8631 (mttm) cc_final: 0.8276 (mttm) REVERT: B 545 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7900 (mptt) REVERT: B 564 LYS cc_start: 0.8872 (mttt) cc_final: 0.8470 (mttt) REVERT: B 571 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 587 MET cc_start: 0.5709 (mtt) cc_final: 0.5185 (mtt) REVERT: B 726 ASP cc_start: 0.7124 (m-30) cc_final: 0.6811 (m-30) REVERT: B 733 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: B 751 MET cc_start: 0.7998 (mmm) cc_final: 0.7333 (mmm) REVERT: B 810 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 865 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6510 (p0) REVERT: B 881 GLU cc_start: 0.7606 (tt0) cc_final: 0.7357 (tm-30) REVERT: B 995 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7495 (tm-30) REVERT: B 1000 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7533 (mmtm) REVERT: B 1027 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6818 (mmtt) REVERT: B 1107 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8209 (tttp) REVERT: B 1108 HIS cc_start: 0.6691 (m170) cc_final: 0.6470 (m170) REVERT: B 1120 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7133 (p0) REVERT: B 1143 LYS cc_start: 0.6946 (mttm) cc_final: 0.6416 (mttm) REVERT: B 1147 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7254 (mm-30) REVERT: B 1255 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 1305 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 1323 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7636 (ptt180) REVERT: B 1416 VAL cc_start: 0.8468 (m) cc_final: 0.8207 (p) REVERT: G 12 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7780 (tt) REVERT: G 13 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8079 (mp) REVERT: G 30 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: G 55 LYS cc_start: 0.8258 (mptt) cc_final: 0.8019 (mttt) REVERT: G 87 GLN cc_start: 0.8185 (tt0) cc_final: 0.7949 (tt0) REVERT: G 130 LYS cc_start: 0.7710 (ttmm) cc_final: 0.7452 (ttmm) REVERT: H 18 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: H 25 GLN cc_start: 0.8119 (tt0) cc_final: 0.7807 (tt0) REVERT: H 93 TYR cc_start: 0.8194 (m-80) cc_final: 0.6479 (m-10) REVERT: H 126 ASP cc_start: 0.8554 (t0) cc_final: 0.7957 (t70) REVERT: H 128 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8149 (mtmm) outliers start: 68 outliers final: 44 residues processed: 445 average time/residue: 0.1756 time to fit residues: 119.7821 Evaluate side-chains 450 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 394 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 294 optimal weight: 0.6980 chunk 58 optimal weight: 50.0000 chunk 118 optimal weight: 0.9990 chunk 193 optimal weight: 0.0670 chunk 300 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 311 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 98 GLN B 306 GLN B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1427 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.219021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166035 restraints weight = 46387.144| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.69 r_work: 0.3685 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31440 Z= 0.139 Angle : 0.542 9.671 43654 Z= 0.291 Chirality : 0.039 0.183 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.143 177.782 7092 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 2.18 % Allowed : 15.40 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.15), residues: 2913 helix: 1.18 (0.15), residues: 1195 sheet: -0.27 (0.27), residues: 352 loop : -0.89 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.031 0.001 TYR A 186 PHE 0.030 0.001 PHE B 478 TRP 0.031 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00305 (31440) covalent geometry : angle 0.54189 (43654) hydrogen bonds : bond 0.03803 ( 1250) hydrogen bonds : angle 4.04943 ( 3290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 399 time to evaluate : 0.820 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: A 13 ASN cc_start: 0.8316 (p0) cc_final: 0.7876 (p0) REVERT: A 94 HIS cc_start: 0.7035 (p90) cc_final: 0.6762 (p90) REVERT: A 107 LYS cc_start: 0.8290 (mttt) cc_final: 0.7986 (mttp) REVERT: A 171 GLU cc_start: 0.6989 (mm-30) cc_final: 0.5144 (mt-10) REVERT: A 181 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.7158 (m-70) REVERT: A 297 TYR cc_start: 0.5052 (t80) cc_final: 0.4688 (t80) REVERT: A 303 ASN cc_start: 0.7197 (t0) cc_final: 0.6590 (p0) REVERT: A 317 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 328 ILE cc_start: 0.7218 (pt) cc_final: 0.6949 (mt) REVERT: A 379 TYR cc_start: 0.7029 (t80) cc_final: 0.6740 (t80) REVERT: A 667 GLU cc_start: 0.7516 (pp20) cc_final: 0.7282 (pp20) REVERT: A 696 ASP cc_start: 0.7982 (t0) cc_final: 0.7444 (t0) REVERT: A 993 MET cc_start: 0.6822 (tpt) cc_final: 0.5771 (tpt) REVERT: A 995 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 1011 LYS cc_start: 0.8526 (ptpt) cc_final: 0.8087 (ptpt) REVERT: A 1037 ASP cc_start: 0.7159 (m-30) cc_final: 0.6914 (m-30) REVERT: A 1099 TRP cc_start: 0.6713 (p90) cc_final: 0.6470 (p90) REVERT: A 1185 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7719 (mtp180) REVERT: A 1211 ASN cc_start: 0.7492 (m110) cc_final: 0.6970 (m110) REVERT: A 1250 LYS cc_start: 0.7862 (mttt) cc_final: 0.7596 (mtmt) REVERT: A 1317 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 1325 LEU cc_start: 0.8140 (mm) cc_final: 0.7857 (mp) REVERT: A 1356 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7532 (mtpp) REVERT: A 1376 GLN cc_start: 0.8050 (pp30) cc_final: 0.7468 (pp30) REVERT: A 1388 LYS cc_start: 0.7955 (tmtt) cc_final: 0.7667 (ttpp) REVERT: A 1436 GLN cc_start: 0.6048 (tp-100) cc_final: 0.5647 (tp-100) REVERT: B 102 GLU cc_start: 0.7287 (mp0) cc_final: 0.6886 (pm20) REVERT: B 168 GLU cc_start: 0.7703 (tp30) cc_final: 0.7217 (tt0) REVERT: B 309 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8125 (mtpp) REVERT: B 383 LEU cc_start: 0.7950 (mm) cc_final: 0.7592 (mp) REVERT: B 425 PHE cc_start: 0.6862 (m-10) cc_final: 0.6639 (m-10) REVERT: B 429 GLN cc_start: 0.7951 (mm-40) cc_final: 0.6763 (mm110) REVERT: B 432 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 476 LYS cc_start: 0.8701 (mttm) cc_final: 0.8282 (mttm) REVERT: B 499 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 545 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7706 (mmtt) REVERT: B 571 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 587 MET cc_start: 0.5690 (mtt) cc_final: 0.5169 (mtt) REVERT: B 726 ASP cc_start: 0.7099 (m-30) cc_final: 0.6768 (m-30) REVERT: B 733 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: B 751 MET cc_start: 0.8000 (mmm) cc_final: 0.7314 (mmm) REVERT: B 865 ASN cc_start: 0.6778 (OUTLIER) cc_final: 0.6526 (p0) REVERT: B 881 GLU cc_start: 0.7565 (tt0) cc_final: 0.7292 (tm-30) REVERT: B 995 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 1000 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7349 (mmtm) REVERT: B 1027 LYS cc_start: 0.7065 (mmmt) cc_final: 0.6511 (mmtm) REVERT: B 1107 LYS cc_start: 0.8455 (ttpt) cc_final: 0.8199 (tttp) REVERT: B 1143 LYS cc_start: 0.6898 (mttm) cc_final: 0.6377 (mttm) REVERT: B 1147 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7249 (mm-30) REVERT: B 1255 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 1305 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7656 (mm-30) REVERT: B 1323 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7644 (ptt180) REVERT: G 12 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7713 (tt) REVERT: G 13 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8065 (mp) REVERT: G 30 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: G 55 LYS cc_start: 0.8244 (mptt) cc_final: 0.7995 (mttt) REVERT: G 87 GLN cc_start: 0.8162 (tt0) cc_final: 0.7937 (tt0) REVERT: H 18 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: H 25 GLN cc_start: 0.8024 (tt0) cc_final: 0.7693 (tt0) REVERT: H 126 ASP cc_start: 0.8540 (t0) cc_final: 0.7869 (t70) REVERT: H 128 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8154 (mtmm) outliers start: 59 outliers final: 41 residues processed: 432 average time/residue: 0.1933 time to fit residues: 128.1505 Evaluate side-chains 440 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 158 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.3980 chunk 288 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 98 GLN B 340 GLN B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN B1427 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.218841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.166092 restraints weight = 46491.034| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.74 r_work: 0.3684 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31440 Z= 0.151 Angle : 0.559 9.446 43654 Z= 0.299 Chirality : 0.040 0.176 4937 Planarity : 0.003 0.040 4540 Dihedral : 20.130 177.601 7090 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 2.04 % Allowed : 16.03 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.16), residues: 2913 helix: 1.19 (0.15), residues: 1196 sheet: -0.21 (0.27), residues: 359 loop : -0.87 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 104 TYR 0.026 0.001 TYR A 186 PHE 0.023 0.001 PHE G 88 TRP 0.028 0.002 TRP B1005 HIS 0.013 0.001 HIS B1108 Details of bonding type rmsd covalent geometry : bond 0.00332 (31440) covalent geometry : angle 0.55870 (43654) hydrogen bonds : bond 0.03924 ( 1250) hydrogen bonds : angle 4.06256 ( 3290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 404 time to evaluate : 0.938 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: A 13 ASN cc_start: 0.8331 (p0) cc_final: 0.7891 (p0) REVERT: A 94 HIS cc_start: 0.7021 (p90) cc_final: 0.6775 (p90) REVERT: A 107 LYS cc_start: 0.8269 (mttt) cc_final: 0.7963 (mttp) REVERT: A 181 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: A 297 TYR cc_start: 0.5174 (t80) cc_final: 0.4758 (t80) REVERT: A 303 ASN cc_start: 0.7206 (t0) cc_final: 0.6619 (p0) REVERT: A 317 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7027 (mm-30) REVERT: A 318 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.6843 (ttp-110) REVERT: A 328 ILE cc_start: 0.7230 (pt) cc_final: 0.6957 (mt) REVERT: A 366 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6066 (mppt) REVERT: A 379 TYR cc_start: 0.7069 (t80) cc_final: 0.6846 (t80) REVERT: A 667 GLU cc_start: 0.7502 (pp20) cc_final: 0.7262 (pp20) REVERT: A 696 ASP cc_start: 0.7987 (t0) cc_final: 0.7422 (t0) REVERT: A 982 TRP cc_start: 0.8190 (t-100) cc_final: 0.7911 (t-100) REVERT: A 993 MET cc_start: 0.6835 (tpt) cc_final: 0.5793 (tpt) REVERT: A 995 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7298 (tm-30) REVERT: A 1011 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8083 (ptpt) REVERT: A 1037 ASP cc_start: 0.7100 (m-30) cc_final: 0.6855 (m-30) REVERT: A 1185 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7731 (mtp180) REVERT: A 1211 ASN cc_start: 0.7455 (m110) cc_final: 0.6956 (m110) REVERT: A 1250 LYS cc_start: 0.7855 (mttt) cc_final: 0.7627 (mtmt) REVERT: A 1287 GLU cc_start: 0.7867 (tt0) cc_final: 0.7441 (tm-30) REVERT: A 1317 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 1325 LEU cc_start: 0.8145 (mm) cc_final: 0.7874 (mp) REVERT: A 1356 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7432 (mtpp) REVERT: A 1376 GLN cc_start: 0.8030 (pp30) cc_final: 0.7430 (pp30) REVERT: A 1388 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7680 (ttpp) REVERT: A 1436 GLN cc_start: 0.6041 (tp-100) cc_final: 0.5628 (tp-100) REVERT: B 102 GLU cc_start: 0.7289 (mp0) cc_final: 0.6955 (pm20) REVERT: B 168 GLU cc_start: 0.7706 (tp30) cc_final: 0.7183 (tt0) REVERT: B 201 PHE cc_start: 0.7885 (t80) cc_final: 0.7663 (t80) REVERT: B 383 LEU cc_start: 0.7959 (mm) cc_final: 0.7595 (mp) REVERT: B 425 PHE cc_start: 0.6890 (m-10) cc_final: 0.6683 (m-10) REVERT: B 432 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7220 (t80) REVERT: B 476 LYS cc_start: 0.8697 (mttm) cc_final: 0.8293 (mttm) REVERT: B 545 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7746 (mmtt) REVERT: B 568 PHE cc_start: 0.8236 (m-10) cc_final: 0.7966 (m-10) REVERT: B 571 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6913 (mt-10) REVERT: B 587 MET cc_start: 0.5677 (mtt) cc_final: 0.5143 (mtt) REVERT: B 726 ASP cc_start: 0.7089 (m-30) cc_final: 0.6768 (m-30) REVERT: B 733 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: B 751 MET cc_start: 0.7937 (mmm) cc_final: 0.7278 (mmm) REVERT: B 810 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7566 (tt) REVERT: B 865 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6505 (p0) REVERT: B 881 GLU cc_start: 0.7583 (tt0) cc_final: 0.7320 (tm-30) REVERT: B 994 ASN cc_start: 0.7332 (m-40) cc_final: 0.7045 (m-40) REVERT: B 995 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 1000 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7118 (mmtm) REVERT: B 1027 LYS cc_start: 0.7067 (mmmt) cc_final: 0.6555 (mmtm) REVERT: B 1107 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8259 (tttp) REVERT: B 1143 LYS cc_start: 0.6843 (mttm) cc_final: 0.6339 (mttm) REVERT: B 1147 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7212 (mm-30) REVERT: B 1255 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 1274 GLU cc_start: 0.7440 (pm20) cc_final: 0.7219 (pm20) REVERT: B 1305 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7688 (mm-30) REVERT: B 1323 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7669 (ptt180) REVERT: G 12 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7781 (tt) REVERT: G 13 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8127 (mp) REVERT: G 30 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6385 (pm20) REVERT: G 55 LYS cc_start: 0.8257 (mptt) cc_final: 0.7996 (mttt) REVERT: G 87 GLN cc_start: 0.8156 (tt0) cc_final: 0.7920 (tt0) REVERT: G 130 LYS cc_start: 0.7767 (ttmm) cc_final: 0.7462 (ttmm) REVERT: H 18 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: H 25 GLN cc_start: 0.8057 (tt0) cc_final: 0.7729 (tt0) outliers start: 55 outliers final: 43 residues processed: 429 average time/residue: 0.1927 time to fit residues: 126.4600 Evaluate side-chains 453 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 401 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 313 optimal weight: 220.0000 chunk 15 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 410 GLN B 710 ASN B 974 GLN ** B1033 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1427 ASN H 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.214982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159819 restraints weight = 46003.281| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.39 r_work: 0.3644 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 31440 Z= 0.343 Angle : 0.684 10.323 43654 Z= 0.364 Chirality : 0.047 0.187 4937 Planarity : 0.005 0.056 4540 Dihedral : 20.266 177.206 7090 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 2.29 % Allowed : 15.88 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.15), residues: 2913 helix: 0.84 (0.15), residues: 1198 sheet: -0.48 (0.26), residues: 352 loop : -1.09 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 104 TYR 0.025 0.002 TYR B 421 PHE 0.028 0.002 PHE G 88 TRP 0.035 0.002 TRP B1005 HIS 0.014 0.002 HIS B1108 Details of bonding type rmsd covalent geometry : bond 0.00753 (31440) covalent geometry : angle 0.68395 (43654) hydrogen bonds : bond 0.05554 ( 1250) hydrogen bonds : angle 4.39032 ( 3290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 413 time to evaluate : 0.884 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: A 13 ASN cc_start: 0.8326 (p0) cc_final: 0.7865 (p0) REVERT: A 94 HIS cc_start: 0.6947 (p90) cc_final: 0.6739 (p90) REVERT: A 107 LYS cc_start: 0.8303 (mttt) cc_final: 0.8047 (mttp) REVERT: A 136 MET cc_start: 0.6971 (tmm) cc_final: 0.6694 (tmm) REVERT: A 165 GLN cc_start: 0.7285 (mt0) cc_final: 0.7084 (mt0) REVERT: A 303 ASN cc_start: 0.7247 (t0) cc_final: 0.6962 (t0) REVERT: A 309 LYS cc_start: 0.7522 (pttp) cc_final: 0.7196 (ptpt) REVERT: A 317 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 328 ILE cc_start: 0.7294 (pt) cc_final: 0.7084 (mp) REVERT: A 667 GLU cc_start: 0.7499 (pp20) cc_final: 0.7261 (pp20) REVERT: A 688 THR cc_start: 0.7778 (m) cc_final: 0.7555 (p) REVERT: A 696 ASP cc_start: 0.8073 (t0) cc_final: 0.7615 (t0) REVERT: A 993 MET cc_start: 0.6792 (tpt) cc_final: 0.5983 (tpt) REVERT: A 995 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 997 THR cc_start: 0.7408 (m) cc_final: 0.6818 (t) REVERT: A 1037 ASP cc_start: 0.7233 (m-30) cc_final: 0.6961 (m-30) REVERT: A 1185 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7748 (mtp180) REVERT: A 1211 ASN cc_start: 0.7466 (m110) cc_final: 0.6999 (m110) REVERT: A 1250 LYS cc_start: 0.7809 (mttt) cc_final: 0.7457 (mtmt) REVERT: A 1317 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 1324 LEU cc_start: 0.8883 (tp) cc_final: 0.8641 (tp) REVERT: A 1325 LEU cc_start: 0.8193 (mm) cc_final: 0.7904 (mp) REVERT: A 1356 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7632 (mtpp) REVERT: A 1376 GLN cc_start: 0.8119 (pp30) cc_final: 0.7501 (pp30) REVERT: A 1383 LYS cc_start: 0.8110 (tttm) cc_final: 0.7829 (tttt) REVERT: A 1388 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7795 (ttpp) REVERT: A 1423 LEU cc_start: 0.8527 (mm) cc_final: 0.7973 (mt) REVERT: A 1431 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7959 (ttmt) REVERT: A 1436 GLN cc_start: 0.6085 (tp-100) cc_final: 0.5664 (tp-100) REVERT: B 41 MET cc_start: 0.8599 (ptt) cc_final: 0.8368 (ptm) REVERT: B 90 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: B 102 GLU cc_start: 0.7240 (mp0) cc_final: 0.6896 (pm20) REVERT: B 168 GLU cc_start: 0.7722 (tp30) cc_final: 0.7229 (tt0) REVERT: B 201 PHE cc_start: 0.7986 (t80) cc_final: 0.7760 (t80) REVERT: B 383 LEU cc_start: 0.7946 (mm) cc_final: 0.7677 (mp) REVERT: B 425 PHE cc_start: 0.7030 (m-10) cc_final: 0.6686 (m-10) REVERT: B 429 GLN cc_start: 0.7869 (mm-40) cc_final: 0.6712 (mm-40) REVERT: B 476 LYS cc_start: 0.8751 (mttm) cc_final: 0.8364 (mttm) REVERT: B 545 LYS cc_start: 0.8177 (mmtp) cc_final: 0.7930 (mptt) REVERT: B 550 LYS cc_start: 0.7166 (mppt) cc_final: 0.6884 (mmmt) REVERT: B 568 PHE cc_start: 0.8346 (m-10) cc_final: 0.8040 (m-10) REVERT: B 571 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6976 (mt-10) REVERT: B 587 MET cc_start: 0.5728 (mtt) cc_final: 0.5242 (mtt) REVERT: B 726 ASP cc_start: 0.7090 (m-30) cc_final: 0.6841 (m-30) REVERT: B 733 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: B 751 MET cc_start: 0.8000 (mmm) cc_final: 0.7348 (mmm) REVERT: B 810 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7562 (tt) REVERT: B 865 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.6580 (p0) REVERT: B 881 GLU cc_start: 0.7818 (tt0) cc_final: 0.7602 (tm-30) REVERT: B 994 ASN cc_start: 0.7341 (m-40) cc_final: 0.7069 (m-40) REVERT: B 995 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 1000 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7142 (mmtm) REVERT: B 1027 LYS cc_start: 0.7147 (mmmt) cc_final: 0.6880 (mmtt) REVERT: B 1107 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8173 (tttp) REVERT: B 1133 LYS cc_start: 0.6869 (tttt) cc_final: 0.6582 (tttp) REVERT: B 1143 LYS cc_start: 0.6890 (mttm) cc_final: 0.6377 (mttm) REVERT: B 1147 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7144 (mm-30) REVERT: B 1305 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 1323 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7700 (ptt180) REVERT: B 1341 GLU cc_start: 0.6541 (tp30) cc_final: 0.6291 (tp30) REVERT: B 1416 VAL cc_start: 0.8501 (m) cc_final: 0.8123 (p) REVERT: G 13 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8048 (mp) REVERT: G 30 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: G 55 LYS cc_start: 0.8274 (mptt) cc_final: 0.8042 (mttt) REVERT: G 87 GLN cc_start: 0.8166 (tt0) cc_final: 0.7957 (tt0) REVERT: G 130 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7297 (ttmm) REVERT: H 18 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: H 25 GLN cc_start: 0.8146 (tt0) cc_final: 0.7818 (tt0) REVERT: H 56 MET cc_start: 0.7092 (mtp) cc_final: 0.6889 (mtp) REVERT: H 93 TYR cc_start: 0.8205 (m-80) cc_final: 0.6635 (m-80) outliers start: 62 outliers final: 42 residues processed: 444 average time/residue: 0.1987 time to fit residues: 134.9503 Evaluate side-chains 454 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 405 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 936 LYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1234 LYS Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1389 THR Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 58 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 316 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 238 optimal weight: 0.0070 chunk 208 optimal weight: 0.5980 chunk 47 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 89 ASN B 98 GLN B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN B 974 GLN G 94 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.218772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166051 restraints weight = 46624.321| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.74 r_work: 0.3682 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31440 Z= 0.138 Angle : 0.582 10.104 43654 Z= 0.310 Chirality : 0.040 0.163 4937 Planarity : 0.004 0.053 4540 Dihedral : 20.177 177.417 7090 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 1.89 % Allowed : 16.95 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.15), residues: 2913 helix: 1.09 (0.15), residues: 1200 sheet: -0.30 (0.26), residues: 359 loop : -0.94 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.043 0.001 TYR A 379 PHE 0.022 0.001 PHE G 88 TRP 0.050 0.002 TRP B1005 HIS 0.015 0.001 HIS B1108 Details of bonding type rmsd covalent geometry : bond 0.00305 (31440) covalent geometry : angle 0.58210 (43654) hydrogen bonds : bond 0.03930 ( 1250) hydrogen bonds : angle 4.12936 ( 3290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10148.11 seconds wall clock time: 173 minutes 52.71 seconds (10432.71 seconds total)