Starting phenix.real_space_refine on Thu Jun 26 03:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wr4_37762/06_2025/8wr4_37762_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wr4_37762/06_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_37762/06_2025/8wr4_37762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wr4_37762/06_2025/8wr4_37762.map" model { file = "/net/cci-nas-00/data/ceres_data/8wr4_37762/06_2025/8wr4_37762_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wr4_37762/06_2025/8wr4_37762_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.84, per 1000 atoms: 0.66 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: 7.29 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 11.84 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: 19.53 Time building geometry restraints manager: 8.41 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: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 84.360 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.140 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.240 ------------------------------------------------------------------------------- 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 : 10.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (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 TRP 0.020 0.001 TRP A 976 HIS 0.007 0.001 HIS A 287 PHE 0.024 0.001 PHE A 140 TYR 0.016 0.001 TYR A 345 ARG 0.007 0.000 ARG B1252 Details of bonding type rmsd hydrogen bonds : bond 0.13222 ( 1250) hydrogen bonds : angle 5.56352 ( 3290) covalent geometry : bond 0.00364 (31440) covalent geometry : angle 0.56621 (43654) *********************** 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 : 2.764 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: 0.5205 time to fit residues: 392.1292 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 : 4.381 ------------------------------------------------------------------------------- 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 268 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 0.0970 chunk 185 optimal weight: 0.0980 chunk 288 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 B 979 ASN G 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.220553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167803 restraints weight = 47073.431| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.67 r_work: 0.3711 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31440 Z= 0.140 Angle : 0.559 9.359 43654 Z= 0.300 Chirality : 0.040 0.211 4937 Planarity : 0.003 0.047 4540 Dihedral : 20.354 179.920 7097 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 1.15 % Allowed : 7.48 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2913 helix: 1.16 (0.15), residues: 1191 sheet: -0.42 (0.27), residues: 346 loop : -0.84 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1005 HIS 0.008 0.001 HIS A 287 PHE 0.031 0.001 PHE B 871 TYR 0.027 0.001 TYR A 345 ARG 0.008 0.000 ARG A1028 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1250) hydrogen bonds : angle 4.45166 ( 3290) covalent geometry : bond 0.00299 (31440) covalent geometry : angle 0.55889 (43654) *********************** 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 469 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 438 time to evaluate : 2.697 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: 0.7210 (p90) cc_final: 0.6904 (p90) REVERT: A 134 ASN cc_start: 0.7752 (m110) cc_final: 0.7444 (m110) REVERT: A 136 MET cc_start: 0.7001 (tmm) cc_final: 0.6711 (tmm) REVERT: A 157 HIS cc_start: 0.6490 (t70) cc_final: 0.6219 (t70) REVERT: A 158 LEU cc_start: 0.6706 (mt) cc_final: 0.6382 (mt) REVERT: A 160 LYS cc_start: 0.7611 (tttp) cc_final: 0.7380 (ttmm) REVERT: A 186 TYR cc_start: 0.6982 (t80) cc_final: 0.6710 (t80) REVERT: A 309 LYS cc_start: 0.7711 (pttp) cc_final: 0.7468 (ptpt) REVERT: A 317 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7228 (mp0) REVERT: A 333 LYS cc_start: 0.7622 (tttp) cc_final: 0.7379 (tptp) REVERT: A 335 PHE cc_start: 0.7982 (m-80) cc_final: 0.7769 (m-10) REVERT: A 667 GLU cc_start: 0.7343 (pp20) cc_final: 0.7109 (pp20) REVERT: A 696 ASP cc_start: 0.7994 (t0) cc_final: 0.7473 (t0) REVERT: A 708 PHE cc_start: 0.8222 (t80) cc_final: 0.7941 (t80) REVERT: A 710 ASN cc_start: 0.7816 (m-40) cc_final: 0.7355 (m-40) REVERT: A 938 ILE cc_start: 0.8640 (tp) cc_final: 0.8399 (tp) REVERT: A 982 TRP cc_start: 0.7959 (t-100) cc_final: 0.7726 (t-100) REVERT: A 993 MET cc_start: 0.6819 (tpt) cc_final: 0.5779 (tpt) REVERT: A 995 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 1011 LYS cc_start: 0.8418 (ptpt) cc_final: 0.8035 (ptpt) REVERT: A 1185 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7736 (mtp180) REVERT: A 1187 SER cc_start: 0.8274 (m) cc_final: 0.8051 (p) REVERT: A 1221 GLU cc_start: 0.7989 (mp0) cc_final: 0.7691 (mp0) REVERT: A 1239 TYR cc_start: 0.7752 (m-80) cc_final: 0.7486 (m-80) REVERT: A 1305 GLU cc_start: 0.7692 (tp30) cc_final: 0.7233 (tm-30) REVERT: A 1317 GLU cc_start: 0.6993 (tp30) cc_final: 0.6701 (tp30) REVERT: A 1323 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7991 (ttp80) REVERT: A 1390 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7938 (mmmt) REVERT: A 1436 GLN cc_start: 0.6109 (tp-100) cc_final: 0.5544 (tp-100) REVERT: B 166 LYS cc_start: 0.8314 (tttt) cc_final: 0.8112 (tttt) REVERT: B 168 GLU cc_start: 0.7757 (tp30) cc_final: 0.7299 (tt0) REVERT: B 169 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7644 (ptpt) REVERT: B 192 ASP cc_start: 0.0587 (OUTLIER) cc_final: 0.0332 (p0) REVERT: B 282 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 298 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: B 383 LEU cc_start: 0.7989 (mm) cc_final: 0.7590 (mp) REVERT: B 432 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.7135 (t80) REVERT: B 476 LYS cc_start: 0.8634 (mttm) cc_final: 0.8228 (mttm) REVERT: B 564 LYS cc_start: 0.8743 (mttt) cc_final: 0.8340 (mttt) REVERT: B 656 MET cc_start: 0.7075 (mpp) cc_final: 0.6870 (mpp) REVERT: B 710 ASN cc_start: 0.7585 (m110) cc_final: 0.7366 (m-40) REVERT: B 726 ASP cc_start: 0.7053 (m-30) cc_final: 0.6765 (m-30) REVERT: B 728 LYS cc_start: 0.7505 (pttm) cc_final: 0.7212 (pmtt) REVERT: B 729 LYS cc_start: 0.8191 (ptmm) cc_final: 0.7684 (pttp) REVERT: B 751 MET cc_start: 0.7819 (mmm) cc_final: 0.7390 (mmm) REVERT: B 923 MET cc_start: 0.6323 (tmm) cc_final: 0.5612 (tmm) REVERT: B 965 ASN cc_start: 0.7056 (p0) cc_final: 0.6804 (p0) REVERT: B 1000 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7460 (mmtm) REVERT: B 1027 LYS cc_start: 0.6825 (mmmt) cc_final: 0.6363 (mmtt) REVERT: B 1108 HIS cc_start: 0.6330 (m170) cc_final: 0.6124 (m170) REVERT: B 1120 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7279 (p0) REVERT: B 1211 ASN cc_start: 0.7349 (m-40) cc_final: 0.6968 (m-40) REVERT: B 1219 ASN cc_start: 0.7600 (t0) cc_final: 0.7392 (t0) REVERT: B 1255 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 1305 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 1323 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7824 (ptt180) REVERT: B 1377 ASP cc_start: 0.7358 (p0) cc_final: 0.7060 (t70) REVERT: B 1416 VAL cc_start: 0.8503 (m) cc_final: 0.8243 (p) REVERT: B 1426 ILE cc_start: 0.8223 (mm) cc_final: 0.7998 (mp) REVERT: B 1427 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.7040 (t0) REVERT: G 13 LEU cc_start: 0.8128 (mm) cc_final: 0.7836 (mp) REVERT: G 30 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6660 (pm20) REVERT: G 48 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8282 (mmmm) REVERT: G 52 ARG cc_start: 0.6315 (tpp80) cc_final: 0.6102 (tpp80) REVERT: H 25 GLN cc_start: 0.7977 (tt0) cc_final: 0.7762 (tt0) REVERT: H 128 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8097 (mtmm) outliers start: 31 outliers final: 16 residues processed: 449 average time/residue: 0.4882 time to fit residues: 331.0784 Evaluate side-chains 434 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 412 time to evaluate : 3.011 ------------------------------------------------------------------------------- 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 323 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1430 THR 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 432 PHE 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 16 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.0670 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN G 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.219679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.166074 restraints weight = 47019.401| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.71 r_work: 0.3690 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31440 Z= 0.161 Angle : 0.557 8.775 43654 Z= 0.299 Chirality : 0.040 0.216 4937 Planarity : 0.003 0.044 4540 Dihedral : 20.261 179.932 7092 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.70 % Rotamer: Outliers : 1.55 % Allowed : 10.62 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2913 helix: 1.19 (0.15), residues: 1194 sheet: -0.33 (0.27), residues: 349 loop : -0.88 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B1005 HIS 0.008 0.001 HIS A 287 PHE 0.020 0.001 PHE G 88 TYR 0.023 0.001 TYR A 353 ARG 0.004 0.000 ARG A1185 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1250) hydrogen bonds : angle 4.23843 ( 3290) covalent geometry : bond 0.00350 (31440) covalent geometry : angle 0.55748 (43654) *********************** 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 457 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 415 time to evaluate : 3.801 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: 0.7179 (p90) cc_final: 0.6903 (p90) REVERT: A 134 ASN cc_start: 0.7747 (m110) cc_final: 0.7437 (m110) REVERT: A 135 GLU cc_start: 0.7801 (tp30) cc_final: 0.7516 (tp30) REVERT: A 136 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6720 (tmm) REVERT: A 186 TYR cc_start: 0.7048 (t80) cc_final: 0.6762 (t80) REVERT: A 317 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7234 (mp0) REVERT: A 334 GLU cc_start: 0.7433 (pt0) cc_final: 0.7221 (pm20) REVERT: A 338 GLU cc_start: 0.7583 (mp0) cc_final: 0.7367 (mp0) REVERT: A 366 LYS cc_start: 0.7168 (mmmt) cc_final: 0.6179 (mppt) REVERT: A 667 GLU cc_start: 0.7394 (pp20) cc_final: 0.7105 (pp20) REVERT: A 696 ASP cc_start: 0.8034 (t0) cc_final: 0.7527 (t0) REVERT: A 708 PHE cc_start: 0.8240 (t80) cc_final: 0.8013 (t80) REVERT: A 710 ASN cc_start: 0.7775 (m-40) cc_final: 0.7300 (m-40) REVERT: A 936 LYS cc_start: 0.7749 (pttt) cc_final: 0.7546 (pttt) REVERT: A 993 MET cc_start: 0.6827 (tpt) cc_final: 0.5788 (tpt) REVERT: A 995 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 1011 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8070 (ptpt) REVERT: A 1099 TRP cc_start: 0.6696 (p90) cc_final: 0.6117 (p90) REVERT: A 1305 GLU cc_start: 0.7650 (tp30) cc_final: 0.7152 (tm-30) REVERT: A 1309 GLN cc_start: 0.7856 (mm110) cc_final: 0.7536 (mm-40) REVERT: A 1317 GLU cc_start: 0.7116 (tp30) cc_final: 0.6895 (tp30) REVERT: A 1323 ARG cc_start: 0.8236 (ttp80) cc_final: 0.8032 (ttp80) REVERT: A 1335 TYR cc_start: 0.7915 (t80) cc_final: 0.7627 (t80) REVERT: A 1376 GLN cc_start: 0.8020 (pp30) cc_final: 0.7650 (pp30) REVERT: A 1383 LYS cc_start: 0.8025 (tttm) cc_final: 0.7797 (tttt) REVERT: A 1436 GLN cc_start: 0.6107 (tp-100) cc_final: 0.5568 (tp-100) REVERT: B 102 GLU cc_start: 0.7292 (mp0) cc_final: 0.6915 (pm20) REVERT: B 168 GLU cc_start: 0.7744 (tp30) cc_final: 0.7415 (mt-10) REVERT: B 201 PHE cc_start: 0.8148 (t80) cc_final: 0.7784 (t80) REVERT: B 282 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 290 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7601 (mtmm) REVERT: B 298 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: B 347 ASP cc_start: 0.6487 (m-30) cc_final: 0.6094 (m-30) REVERT: B 383 LEU cc_start: 0.7985 (mm) cc_final: 0.7603 (mp) REVERT: B 476 LYS cc_start: 0.8599 (mttm) cc_final: 0.8173 (mttm) REVERT: B 499 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 545 LYS cc_start: 0.8098 (mptt) cc_final: 0.7854 (mmtp) REVERT: B 564 LYS cc_start: 0.8812 (mttt) cc_final: 0.8410 (mttt) REVERT: B 656 MET cc_start: 0.7056 (mpp) cc_final: 0.6796 (mpp) REVERT: B 710 ASN cc_start: 0.7645 (m110) cc_final: 0.7368 (m110) REVERT: B 726 ASP cc_start: 0.6998 (m-30) cc_final: 0.6665 (m-30) REVERT: B 728 LYS cc_start: 0.7528 (pttm) cc_final: 0.7307 (pmtt) REVERT: B 733 GLN cc_start: 0.7405 (mp10) cc_final: 0.7020 (mp10) REVERT: B 751 MET cc_start: 0.7906 (mmm) cc_final: 0.7470 (mmm) REVERT: B 865 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6517 (p0) REVERT: B 881 GLU cc_start: 0.7536 (tt0) cc_final: 0.7184 (tm-30) REVERT: B 923 MET cc_start: 0.6267 (tmm) cc_final: 0.6053 (tmm) REVERT: B 1000 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7483 (mmtm) REVERT: B 1027 LYS cc_start: 0.6826 (mmmt) cc_final: 0.6519 (mmtt) REVERT: B 1108 HIS cc_start: 0.6537 (m170) cc_final: 0.6265 (m170) REVERT: B 1120 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7140 (p0) REVERT: B 1188 LEU cc_start: 0.8559 (tp) cc_final: 0.8352 (mt) REVERT: B 1211 ASN cc_start: 0.7316 (m-40) cc_final: 0.6967 (m-40) REVERT: B 1219 ASN cc_start: 0.7810 (t0) cc_final: 0.7461 (t0) REVERT: B 1255 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 1305 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 1323 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7708 (ptt180) REVERT: B 1416 VAL cc_start: 0.8493 (m) cc_final: 0.8256 (p) REVERT: B 1427 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7031 (t0) REVERT: G 5 LYS cc_start: 0.6677 (mtpp) cc_final: 0.6442 (mtpp) REVERT: G 13 LEU cc_start: 0.8235 (mm) cc_final: 0.7901 (mp) REVERT: G 30 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: G 48 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8281 (mmmm) REVERT: G 112 THR cc_start: 0.8516 (m) cc_final: 0.8216 (p) REVERT: G 130 LYS cc_start: 0.7499 (ttmm) cc_final: 0.7278 (ttmm) REVERT: H 25 GLN cc_start: 0.8031 (tt0) cc_final: 0.7738 (tt0) REVERT: H 126 ASP cc_start: 0.8597 (t0) cc_final: 0.7929 (t70) REVERT: H 128 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8116 (mtmm) outliers start: 42 outliers final: 20 residues processed: 434 average time/residue: 0.6987 time to fit residues: 466.3445 Evaluate side-chains 425 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 399 time to evaluate : 2.717 ------------------------------------------------------------------------------- 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 934 ILE Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 302 GLN 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 714 ILE 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 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 1423 LEU 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 116 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 67 optimal weight: 0.0060 chunk 243 optimal weight: 0.4980 chunk 217 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 332 GLN A 651 HIS A 685 GLN A1152 ASN B 739 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.220641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166475 restraints weight = 47020.944| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.36 r_work: 0.3745 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2188 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= 0.125 Angle : 0.520 8.986 43654 Z= 0.280 Chirality : 0.039 0.208 4937 Planarity : 0.003 0.042 4540 Dihedral : 20.199 179.400 7092 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 1.59 % Allowed : 12.40 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2913 helix: 1.24 (0.15), residues: 1204 sheet: -0.32 (0.27), residues: 343 loop : -0.85 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1005 HIS 0.008 0.001 HIS A 287 PHE 0.026 0.001 PHE B1073 TYR 0.030 0.001 TYR A1239 ARG 0.006 0.000 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 1250) hydrogen bonds : angle 4.08862 ( 3290) covalent geometry : bond 0.00269 (31440) covalent geometry : angle 0.51981 (43654) *********************** 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 450 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 407 time to evaluate : 2.603 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: 0.7048 (p-80) cc_final: 0.6831 (p90) REVERT: A 134 ASN cc_start: 0.7640 (m110) cc_final: 0.7346 (m110) REVERT: A 136 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6595 (tmm) REVERT: A 171 GLU cc_start: 0.6946 (mm-30) cc_final: 0.5218 (mt-10) REVERT: A 297 TYR cc_start: 0.5541 (t80) cc_final: 0.5320 (t80) REVERT: A 317 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7169 (mp0) REVERT: A 334 GLU cc_start: 0.7335 (pt0) cc_final: 0.7112 (pm20) REVERT: A 335 PHE cc_start: 0.7674 (m-10) cc_final: 0.7447 (m-10) REVERT: A 667 GLU cc_start: 0.7360 (pp20) cc_final: 0.7079 (pp20) REVERT: A 696 ASP cc_start: 0.7995 (t0) cc_final: 0.7462 (t0) REVERT: A 708 PHE cc_start: 0.8188 (t80) cc_final: 0.7980 (t80) REVERT: A 710 ASN cc_start: 0.7614 (m-40) cc_final: 0.7173 (m110) REVERT: A 993 MET cc_start: 0.6773 (tpt) cc_final: 0.5740 (tpt) REVERT: A 995 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 1011 LYS cc_start: 0.8405 (ptpt) cc_final: 0.7965 (ptpt) REVERT: A 1099 TRP cc_start: 0.6611 (p90) cc_final: 0.6087 (p90) REVERT: A 1335 TYR cc_start: 0.7839 (t80) cc_final: 0.7574 (t80) REVERT: A 1356 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7446 (mtpp) REVERT: A 1436 GLN cc_start: 0.5962 (tp-100) cc_final: 0.5488 (tp-100) REVERT: B 168 GLU cc_start: 0.7656 (tp30) cc_final: 0.7181 (tt0) REVERT: B 201 PHE cc_start: 0.8109 (t80) cc_final: 0.7799 (t80) REVERT: B 282 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 290 LYS cc_start: 0.7943 (mmmt) cc_final: 0.7580 (mtmm) REVERT: B 347 ASP cc_start: 0.6424 (m-30) cc_final: 0.6041 (m-30) REVERT: B 383 LEU cc_start: 0.7924 (mm) cc_final: 0.7534 (mp) REVERT: B 425 PHE cc_start: 0.6633 (m-10) cc_final: 0.6173 (m-10) REVERT: B 432 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 476 LYS cc_start: 0.8498 (mttm) cc_final: 0.8094 (mttm) REVERT: B 499 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7317 (mm-30) REVERT: B 564 LYS cc_start: 0.8755 (mttt) cc_final: 0.8339 (mttt) REVERT: B 656 MET cc_start: 0.7029 (mpp) cc_final: 0.6759 (mpp) REVERT: B 710 ASN cc_start: 0.7619 (m110) cc_final: 0.7351 (m110) REVERT: B 726 ASP cc_start: 0.7026 (m-30) cc_final: 0.6738 (m-30) REVERT: B 730 LEU cc_start: 0.8276 (tt) cc_final: 0.7787 (tt) REVERT: B 751 MET cc_start: 0.7882 (mmm) cc_final: 0.7218 (mmm) REVERT: B 865 ASN cc_start: 0.6755 (OUTLIER) cc_final: 0.6499 (p0) REVERT: B 923 MET cc_start: 0.6231 (tmm) cc_final: 0.6017 (tmm) REVERT: B 1000 LYS cc_start: 0.7867 (mmtm) cc_final: 0.7436 (mmtm) REVERT: B 1027 LYS cc_start: 0.6767 (mmmt) cc_final: 0.6480 (mmtt) REVERT: B 1108 HIS cc_start: 0.6418 (m170) cc_final: 0.6164 (m170) REVERT: B 1120 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.7002 (p0) REVERT: B 1188 LEU cc_start: 0.8563 (tp) cc_final: 0.8328 (mt) REVERT: B 1211 ASN cc_start: 0.7308 (m-40) cc_final: 0.6976 (m-40) REVERT: B 1219 ASN cc_start: 0.7793 (t0) cc_final: 0.7408 (t0) REVERT: B 1255 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 1305 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 1323 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7685 (ptt180) REVERT: B 1377 ASP cc_start: 0.7080 (p0) cc_final: 0.6608 (t0) REVERT: B 1416 VAL cc_start: 0.8453 (m) cc_final: 0.8214 (p) REVERT: G 5 LYS cc_start: 0.6634 (mtpp) cc_final: 0.6413 (mtpp) REVERT: G 6 ILE cc_start: 0.7995 (mm) cc_final: 0.7555 (tt) REVERT: G 9 ASP cc_start: 0.7463 (t70) cc_final: 0.7252 (t70) REVERT: G 13 LEU cc_start: 0.8247 (mm) cc_final: 0.7944 (mp) REVERT: G 30 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: G 112 THR cc_start: 0.8436 (m) cc_final: 0.8177 (p) REVERT: G 123 MET cc_start: 0.7685 (tmm) cc_final: 0.6568 (ptm) REVERT: G 130 LYS cc_start: 0.7452 (ttmm) cc_final: 0.7244 (ttmm) REVERT: H 25 GLN cc_start: 0.7891 (tt0) cc_final: 0.7579 (tt0) REVERT: H 126 ASP cc_start: 0.8542 (t0) cc_final: 0.7760 (t0) REVERT: H 128 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8083 (mtmm) outliers start: 43 outliers final: 26 residues processed: 430 average time/residue: 0.5227 time to fit residues: 342.6041 Evaluate side-chains 419 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 388 time to evaluate : 4.660 ------------------------------------------------------------------------------- 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 323 GLU Chi-restraints excluded: chain A residue 685 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1325 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 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 729 LYS 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 1097 LYS 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 B residue 1423 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 116 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 241 optimal weight: 0.9980 chunk 265 optimal weight: 20.0000 chunk 30 optimal weight: 0.0980 chunk 233 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 25 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 0.0020 chunk 198 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN A1152 ASN B 477 HIS B 675 GLN B1427 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.219063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165739 restraints weight = 46832.518| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.76 r_work: 0.3691 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 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 = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31440 Z= 0.167 Angle : 0.542 8.546 43654 Z= 0.293 Chirality : 0.040 0.205 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.171 178.945 7092 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 1.96 % Allowed : 12.73 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 2913 helix: 1.21 (0.15), residues: 1201 sheet: -0.35 (0.27), residues: 355 loop : -0.88 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 PHE 0.019 0.001 PHE B 462 TYR 0.024 0.001 TYR A 379 ARG 0.006 0.000 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 1250) hydrogen bonds : angle 4.10486 ( 3290) covalent geometry : bond 0.00363 (31440) covalent geometry : angle 0.54193 (43654) *********************** 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 466 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 413 time to evaluate : 2.620 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: 0.7009 (p-80) cc_final: 0.6808 (p90) REVERT: A 134 ASN cc_start: 0.7722 (m110) cc_final: 0.7411 (m110) REVERT: A 171 GLU cc_start: 0.7066 (mm-30) cc_final: 0.5390 (mt-10) REVERT: A 303 ASN cc_start: 0.7108 (t0) cc_final: 0.6303 (p0) REVERT: A 317 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7213 (mp0) REVERT: A 366 LYS cc_start: 0.7334 (mmmt) cc_final: 0.6178 (mppt) REVERT: A 379 TYR cc_start: 0.7094 (t80) cc_final: 0.6873 (t80) REVERT: A 667 GLU cc_start: 0.7436 (pp20) cc_final: 0.7135 (pp20) REVERT: A 696 ASP cc_start: 0.8065 (t0) cc_final: 0.7524 (t0) REVERT: A 993 MET cc_start: 0.6849 (tpt) cc_final: 0.5830 (tpt) REVERT: A 995 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 1011 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8063 (ptpt) REVERT: A 1250 LYS cc_start: 0.8091 (mttt) cc_final: 0.7685 (mtmm) REVERT: A 1305 GLU cc_start: 0.7611 (tp30) cc_final: 0.7074 (tm-30) REVERT: A 1309 GLN cc_start: 0.7892 (mm110) cc_final: 0.7681 (mm-40) REVERT: A 1335 TYR cc_start: 0.7873 (t80) cc_final: 0.7598 (t80) REVERT: A 1356 LYS cc_start: 0.7947 (mmtp) cc_final: 0.7432 (mtpp) REVERT: A 1410 ARG cc_start: 0.5490 (ttt90) cc_final: 0.5191 (ttt90) REVERT: A 1436 GLN cc_start: 0.6041 (tp-100) cc_final: 0.5574 (tp-100) REVERT: B 102 GLU cc_start: 0.7285 (mp0) cc_final: 0.6879 (pm20) REVERT: B 168 GLU cc_start: 0.7681 (tp30) cc_final: 0.7259 (tt0) REVERT: B 201 PHE cc_start: 0.8060 (t80) cc_final: 0.7773 (t80) REVERT: B 282 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 347 ASP cc_start: 0.6471 (m-30) cc_final: 0.6097 (m-30) REVERT: B 383 LEU cc_start: 0.7963 (mm) cc_final: 0.7599 (mp) REVERT: B 432 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7191 (t80) REVERT: B 476 LYS cc_start: 0.8546 (mttm) cc_final: 0.8127 (mttm) REVERT: B 499 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 564 LYS cc_start: 0.8865 (mttt) cc_final: 0.8456 (mttt) REVERT: B 656 MET cc_start: 0.7036 (mpp) cc_final: 0.6746 (mpp) REVERT: B 710 ASN cc_start: 0.7667 (m110) cc_final: 0.7389 (m110) REVERT: B 726 ASP cc_start: 0.7100 (m-30) cc_final: 0.6824 (m-30) REVERT: B 730 LEU cc_start: 0.8220 (tt) cc_final: 0.7843 (tt) REVERT: B 733 GLN cc_start: 0.7350 (mp10) cc_final: 0.7149 (mp10) REVERT: B 739 ASN cc_start: 0.7658 (m110) cc_final: 0.7185 (p0) REVERT: B 751 MET cc_start: 0.7911 (mmm) cc_final: 0.7243 (mmm) REVERT: B 865 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6498 (p0) REVERT: B 881 GLU cc_start: 0.7562 (tt0) cc_final: 0.7274 (tm-30) REVERT: B 923 MET cc_start: 0.6349 (tmm) cc_final: 0.6097 (tmm) REVERT: B 1000 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7653 (mmtm) REVERT: B 1027 LYS cc_start: 0.6930 (mmmt) cc_final: 0.6496 (mmtt) REVERT: B 1120 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7157 (p0) REVERT: B 1219 ASN cc_start: 0.7950 (t0) cc_final: 0.7580 (t0) REVERT: B 1255 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 1305 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 1323 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7683 (ptt180) REVERT: B 1377 ASP cc_start: 0.7089 (p0) cc_final: 0.6546 (t0) REVERT: B 1416 VAL cc_start: 0.8472 (m) cc_final: 0.8219 (p) REVERT: G 9 ASP cc_start: 0.7540 (t70) cc_final: 0.7296 (t70) REVERT: G 13 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7953 (mp) REVERT: G 30 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: G 130 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7314 (ttmm) REVERT: H 18 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: H 25 GLN cc_start: 0.7940 (tt0) cc_final: 0.7598 (tt0) REVERT: H 126 ASP cc_start: 0.8571 (t0) cc_final: 0.7835 (t0) REVERT: H 128 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8140 (mtmm) outliers start: 53 outliers final: 36 residues processed: 434 average time/residue: 0.4883 time to fit residues: 320.0682 Evaluate side-chains 435 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 393 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 685 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1195 LYS Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1325 LEU 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 340 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 531 ILE Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET 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 B residue 1423 LEU 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 67 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 116 SER 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 47 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 182 optimal weight: 30.0000 chunk 71 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 359 HIS B 477 HIS B1033 HIS B1427 ASN G 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.215612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161892 restraints weight = 46342.706| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.82 r_work: 0.3623 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 31440 Z= 0.334 Angle : 0.660 10.762 43654 Z= 0.354 Chirality : 0.046 0.214 4937 Planarity : 0.004 0.050 4540 Dihedral : 20.290 178.116 7088 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.12 % Rotamer: Outliers : 2.04 % Allowed : 13.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 2913 helix: 0.81 (0.15), residues: 1194 sheet: -0.39 (0.27), residues: 349 loop : -1.03 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B1005 HIS 0.015 0.002 HIS B 477 PHE 0.030 0.002 PHE G 88 TYR 0.023 0.002 TYR A 379 ARG 0.009 0.001 ARG B 761 Details of bonding type rmsd hydrogen bonds : bond 0.05448 ( 1250) hydrogen bonds : angle 4.37484 ( 3290) covalent geometry : bond 0.00731 (31440) covalent geometry : angle 0.66043 (43654) *********************** 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 472 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 2.987 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: 0.8406 (p0) cc_final: 0.8001 (p0) REVERT: A 134 ASN cc_start: 0.7800 (m110) cc_final: 0.7493 (m110) REVERT: A 136 MET cc_start: 0.7149 (tmm) cc_final: 0.6845 (tmm) REVERT: A 297 TYR cc_start: 0.5336 (t80) cc_final: 0.4891 (t80) REVERT: A 317 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 328 ILE cc_start: 0.7360 (pt) cc_final: 0.7118 (mp) REVERT: A 379 TYR cc_start: 0.7152 (t80) cc_final: 0.6892 (t80) REVERT: A 667 GLU cc_start: 0.7518 (pp20) cc_final: 0.7199 (pp20) REVERT: A 688 THR cc_start: 0.7770 (m) cc_final: 0.7559 (p) REVERT: A 695 LYS cc_start: 0.8449 (tmmt) cc_final: 0.8041 (tmmt) REVERT: A 696 ASP cc_start: 0.8094 (t0) cc_final: 0.7536 (t0) REVERT: A 936 LYS cc_start: 0.7894 (pttt) cc_final: 0.7636 (pttt) REVERT: A 993 MET cc_start: 0.6915 (tpt) cc_final: 0.5853 (tpt) REVERT: A 995 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 1011 LYS cc_start: 0.8548 (ptpt) cc_final: 0.8128 (ptpt) REVERT: A 1172 TRP cc_start: 0.8415 (p90) cc_final: 0.7803 (p90) REVERT: A 1211 ASN cc_start: 0.7506 (m110) cc_final: 0.6967 (m110) REVERT: A 1250 LYS cc_start: 0.7995 (mttt) cc_final: 0.7677 (mtmm) REVERT: A 1305 GLU cc_start: 0.7648 (tp30) cc_final: 0.7203 (tm-30) REVERT: A 1335 TYR cc_start: 0.7882 (t80) cc_final: 0.7642 (t80) REVERT: A 1356 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7630 (mtpp) REVERT: A 1376 GLN cc_start: 0.8099 (pp30) cc_final: 0.7687 (pp30) REVERT: A 1388 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7832 (ttpp) REVERT: A 1436 GLN cc_start: 0.6191 (tp-100) cc_final: 0.5772 (tp-100) REVERT: B 102 GLU cc_start: 0.7303 (mp0) cc_final: 0.6874 (pm20) REVERT: B 168 GLU cc_start: 0.7785 (tp30) cc_final: 0.7268 (tt0) REVERT: B 169 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7688 (ptpt) REVERT: B 182 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7898 (mtpp) REVERT: B 201 PHE cc_start: 0.7963 (t80) cc_final: 0.7671 (t80) REVERT: B 290 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7856 (mmmt) REVERT: B 347 ASP cc_start: 0.6598 (m-30) cc_final: 0.6266 (m-30) REVERT: B 365 LYS cc_start: 0.7378 (mmpt) cc_final: 0.7160 (mmpt) REVERT: B 383 LEU cc_start: 0.7980 (mm) cc_final: 0.7724 (mp) REVERT: B 476 LYS cc_start: 0.8545 (mttm) cc_final: 0.8145 (mttm) REVERT: B 499 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 564 LYS cc_start: 0.8927 (mttt) cc_final: 0.8545 (mttt) REVERT: B 656 MET cc_start: 0.7089 (mpp) cc_final: 0.6750 (mpp) REVERT: B 710 ASN cc_start: 0.7586 (m110) cc_final: 0.7294 (m110) REVERT: B 726 ASP cc_start: 0.7137 (m-30) cc_final: 0.6848 (m-30) REVERT: B 728 LYS cc_start: 0.7968 (pttt) cc_final: 0.7747 (pttm) REVERT: B 751 MET cc_start: 0.7951 (mmm) cc_final: 0.7287 (mmm) REVERT: B 865 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6606 (p0) REVERT: B 881 GLU cc_start: 0.7739 (tt0) cc_final: 0.7457 (tm-30) REVERT: B 923 MET cc_start: 0.6557 (tmm) cc_final: 0.6266 (tmm) REVERT: B 1000 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7655 (mmtm) REVERT: B 1027 LYS cc_start: 0.7217 (mmmt) cc_final: 0.6800 (mmtm) REVERT: B 1110 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8409 (tt) REVERT: B 1120 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (p0) REVERT: B 1132 GLU cc_start: 0.7149 (pp20) cc_final: 0.6766 (pt0) REVERT: B 1135 VAL cc_start: 0.7535 (m) cc_final: 0.7303 (t) REVERT: B 1143 LYS cc_start: 0.6986 (mttm) cc_final: 0.6662 (mttm) REVERT: B 1147 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7272 (mm-30) REVERT: B 1255 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 1305 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 1323 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7695 (ptt180) REVERT: B 1416 VAL cc_start: 0.8512 (m) cc_final: 0.8106 (p) REVERT: G 13 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8034 (mp) REVERT: G 30 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: G 48 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8296 (mmmm) REVERT: G 130 LYS cc_start: 0.7630 (ttmm) cc_final: 0.7311 (ttmm) REVERT: H 18 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: H 25 GLN cc_start: 0.8118 (tt0) cc_final: 0.7791 (tt0) REVERT: H 93 TYR cc_start: 0.8242 (m-80) cc_final: 0.6631 (m-80) REVERT: H 126 ASP cc_start: 0.8663 (t0) cc_final: 0.8051 (t0) REVERT: H 128 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8153 (mtmm) outliers start: 55 outliers final: 38 residues processed: 447 average time/residue: 0.4943 time to fit residues: 336.7295 Evaluate side-chains 441 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 2.894 ------------------------------------------------------------------------------- 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 934 ILE 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 81 LEU 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 301 LEU Chi-restraints excluded: chain B residue 340 GLN 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 531 ILE Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 916 MET Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1110 LEU 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 1256 LEU Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1423 LEU 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 73 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 116 SER 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 85 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 140 optimal weight: 0.0970 chunk 281 optimal weight: 0.9980 chunk 26 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 98 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN B 974 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.218643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.166157 restraints weight = 46620.914| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.78 r_work: 0.3685 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 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 = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31440 Z= 0.143 Angle : 0.554 9.752 43654 Z= 0.297 Chirality : 0.040 0.196 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.166 178.151 7088 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.78 % Allowed : 15.43 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2913 helix: 1.06 (0.15), residues: 1203 sheet: -0.31 (0.27), residues: 351 loop : -0.89 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B1005 HIS 0.016 0.001 HIS A 94 PHE 0.029 0.001 PHE A 708 TYR 0.019 0.001 TYR A1239 ARG 0.006 0.000 ARG B 761 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 1250) hydrogen bonds : angle 4.10109 ( 3290) covalent geometry : bond 0.00313 (31440) covalent geometry : angle 0.55408 (43654) *********************** 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 450 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 2.925 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: A 13 ASN cc_start: 0.8427 (p0) cc_final: 0.8006 (p0) REVERT: A 134 ASN cc_start: 0.7750 (m110) cc_final: 0.7423 (m110) REVERT: A 171 GLU cc_start: 0.7051 (mm-30) cc_final: 0.5385 (mt-10) REVERT: A 297 TYR cc_start: 0.5232 (t80) cc_final: 0.4769 (t80) REVERT: A 303 ASN cc_start: 0.7264 (t0) cc_final: 0.6517 (p0) REVERT: A 309 LYS cc_start: 0.7667 (pttp) cc_final: 0.7410 (ptmt) REVERT: A 317 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7187 (mm-30) REVERT: A 328 ILE cc_start: 0.7321 (pt) cc_final: 0.7068 (mt) REVERT: A 366 LYS cc_start: 0.7326 (mmmt) cc_final: 0.6173 (mppt) REVERT: A 667 GLU cc_start: 0.7504 (pp20) cc_final: 0.7218 (pp20) REVERT: A 688 THR cc_start: 0.7640 (m) cc_final: 0.7400 (p) REVERT: A 696 ASP cc_start: 0.7992 (t0) cc_final: 0.7476 (t0) REVERT: A 993 MET cc_start: 0.6821 (tpt) cc_final: 0.5774 (tpt) REVERT: A 995 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 1011 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8046 (ptpt) REVERT: A 1099 TRP cc_start: 0.6696 (p90) cc_final: 0.6326 (p90) REVERT: A 1172 TRP cc_start: 0.8217 (p90) cc_final: 0.7772 (p90) REVERT: A 1211 ASN cc_start: 0.7430 (m110) cc_final: 0.6902 (m110) REVERT: A 1250 LYS cc_start: 0.8015 (mttt) cc_final: 0.7659 (mtmm) REVERT: A 1305 GLU cc_start: 0.7654 (tp30) cc_final: 0.7208 (tm-30) REVERT: A 1335 TYR cc_start: 0.7850 (t80) cc_final: 0.7556 (t80) REVERT: A 1341 GLU cc_start: 0.6728 (pp20) cc_final: 0.6429 (tm-30) REVERT: A 1356 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7470 (mtpp) REVERT: A 1376 GLN cc_start: 0.8075 (pp30) cc_final: 0.7719 (pp30) REVERT: A 1400 LEU cc_start: 0.8033 (mm) cc_final: 0.7822 (mt) REVERT: A 1436 GLN cc_start: 0.6060 (tp-100) cc_final: 0.5666 (tp-100) REVERT: B 102 GLU cc_start: 0.7290 (mp0) cc_final: 0.6973 (pm20) REVERT: B 168 GLU cc_start: 0.7739 (tp30) cc_final: 0.7293 (tt0) REVERT: B 201 PHE cc_start: 0.7931 (t80) cc_final: 0.7726 (t80) REVERT: B 338 GLU cc_start: 0.7240 (mp0) cc_final: 0.6537 (mt-10) REVERT: B 340 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: B 365 LYS cc_start: 0.7299 (mmpt) cc_final: 0.7085 (mmpt) REVERT: B 374 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 383 LEU cc_start: 0.7960 (mm) cc_final: 0.7601 (mp) REVERT: B 432 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 476 LYS cc_start: 0.8539 (mttm) cc_final: 0.8151 (mttm) REVERT: B 499 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 564 LYS cc_start: 0.8864 (mttt) cc_final: 0.8469 (mttt) REVERT: B 656 MET cc_start: 0.7008 (mpp) cc_final: 0.6688 (mpp) REVERT: B 726 ASP cc_start: 0.7098 (m-30) cc_final: 0.6858 (m-30) REVERT: B 728 LYS cc_start: 0.7834 (pttt) cc_final: 0.7545 (ptpt) REVERT: B 733 GLN cc_start: 0.7509 (mp10) cc_final: 0.7306 (mp10) REVERT: B 751 MET cc_start: 0.7945 (mmm) cc_final: 0.7277 (mmm) REVERT: B 810 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7620 (tt) REVERT: B 865 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6497 (p0) REVERT: B 923 MET cc_start: 0.6521 (tmm) cc_final: 0.6191 (tmm) REVERT: B 1000 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7560 (mmtm) REVERT: B 1027 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6866 (mmtt) REVERT: B 1120 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.7101 (p0) REVERT: B 1143 LYS cc_start: 0.6935 (mttm) cc_final: 0.6385 (mttm) REVERT: B 1147 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7038 (mm-30) REVERT: B 1255 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 1305 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 1323 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7623 (ptt180) REVERT: B 1377 ASP cc_start: 0.7089 (p0) cc_final: 0.6681 (t0) REVERT: B 1416 VAL cc_start: 0.8488 (m) cc_final: 0.8194 (p) REVERT: B 1440 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7207 (mt-10) REVERT: G 13 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (mp) REVERT: G 30 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: G 123 MET cc_start: 0.7763 (tmm) cc_final: 0.6362 (ptm) REVERT: H 18 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: H 25 GLN cc_start: 0.8041 (tt0) cc_final: 0.7712 (tt0) REVERT: H 93 TYR cc_start: 0.8175 (m-80) cc_final: 0.6417 (m-10) REVERT: H 126 ASP cc_start: 0.8583 (t0) cc_final: 0.7857 (t0) REVERT: H 128 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8148 (mtmm) outliers start: 48 outliers final: 30 residues processed: 426 average time/residue: 0.4778 time to fit residues: 308.7732 Evaluate side-chains 428 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 2.884 ------------------------------------------------------------------------------- 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 934 ILE Chi-restraints excluded: chain A residue 1175 VAL 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 98 GLN 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 340 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 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU 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 1025 SER 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 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 67 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 50.0000 chunk 251 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 298 optimal weight: 50.0000 chunk 190 optimal weight: 0.5980 chunk 207 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 410 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1427 ASN G 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.216063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.162555 restraints weight = 46354.023| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.73 r_work: 0.3637 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 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 = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31440 Z= 0.269 Angle : 0.627 10.532 43654 Z= 0.335 Chirality : 0.044 0.204 4937 Planarity : 0.004 0.044 4540 Dihedral : 20.240 177.590 7088 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 2.04 % Allowed : 15.62 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2913 helix: 0.90 (0.15), residues: 1196 sheet: -0.36 (0.27), residues: 351 loop : -1.01 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1005 HIS 0.010 0.001 HIS B1108 PHE 0.030 0.002 PHE A 708 TYR 0.025 0.002 TYR A 353 ARG 0.006 0.001 ARG B1408 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 1250) hydrogen bonds : angle 4.27993 ( 3290) covalent geometry : bond 0.00591 (31440) covalent geometry : angle 0.62673 (43654) *********************** 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 454 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 399 time to evaluate : 2.955 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: A 13 ASN cc_start: 0.8433 (p0) cc_final: 0.7975 (p0) REVERT: A 134 ASN cc_start: 0.7822 (m110) cc_final: 0.7505 (m110) REVERT: A 136 MET cc_start: 0.7108 (tmm) cc_final: 0.6681 (tmm) REVERT: A 181 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7317 (m-70) REVERT: A 186 TYR cc_start: 0.7093 (t80) cc_final: 0.6708 (t80) REVERT: A 297 TYR cc_start: 0.5290 (t80) cc_final: 0.4859 (t80) REVERT: A 303 ASN cc_start: 0.7333 (t0) cc_final: 0.6598 (p0) REVERT: A 309 LYS cc_start: 0.7606 (pttp) cc_final: 0.7283 (ptpt) REVERT: A 317 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 328 ILE cc_start: 0.7328 (pt) cc_final: 0.7101 (mp) REVERT: A 333 LYS cc_start: 0.7973 (tptp) cc_final: 0.7605 (tppt) REVERT: A 379 TYR cc_start: 0.7100 (t80) cc_final: 0.6732 (t80) REVERT: A 380 GLN cc_start: 0.7717 (tt0) cc_final: 0.7474 (tt0) REVERT: A 667 GLU cc_start: 0.7469 (pp20) cc_final: 0.7202 (pp20) REVERT: A 688 THR cc_start: 0.7764 (m) cc_final: 0.7554 (p) REVERT: A 696 ASP cc_start: 0.8043 (t0) cc_final: 0.7515 (t0) REVERT: A 993 MET cc_start: 0.6820 (tpt) cc_final: 0.5799 (tpt) REVERT: A 995 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 1011 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8139 (ptpt) REVERT: A 1099 TRP cc_start: 0.6757 (p90) cc_final: 0.6475 (p90) REVERT: A 1172 TRP cc_start: 0.8422 (p90) cc_final: 0.7904 (p90) REVERT: A 1211 ASN cc_start: 0.7496 (m110) cc_final: 0.6977 (m110) REVERT: A 1250 LYS cc_start: 0.7974 (mttt) cc_final: 0.7704 (mtmm) REVERT: A 1317 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7032 (mm-30) REVERT: A 1341 GLU cc_start: 0.6908 (pp20) cc_final: 0.6201 (tm-30) REVERT: A 1356 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7703 (mtpp) REVERT: A 1376 GLN cc_start: 0.8162 (pp30) cc_final: 0.7658 (pp30) REVERT: A 1436 GLN cc_start: 0.6088 (tp-100) cc_final: 0.5693 (tp-100) REVERT: B 90 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 168 GLU cc_start: 0.7744 (tp30) cc_final: 0.7237 (tt0) REVERT: B 201 PHE cc_start: 0.7958 (t80) cc_final: 0.7691 (t80) REVERT: B 326 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7818 (ttm-80) REVERT: B 340 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6931 (mt0) REVERT: B 347 ASP cc_start: 0.6429 (m-30) cc_final: 0.6225 (m-30) REVERT: B 365 LYS cc_start: 0.7354 (mmpt) cc_final: 0.7135 (mmpt) REVERT: B 374 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 383 LEU cc_start: 0.7958 (mm) cc_final: 0.7673 (mp) REVERT: B 467 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7865 (pttp) REVERT: B 476 LYS cc_start: 0.8564 (mttm) cc_final: 0.8144 (mttm) REVERT: B 499 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 564 LYS cc_start: 0.8937 (mttt) cc_final: 0.8553 (mttt) REVERT: B 568 PHE cc_start: 0.8338 (m-10) cc_final: 0.8071 (m-10) REVERT: B 571 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 656 MET cc_start: 0.7086 (mpp) cc_final: 0.6754 (mpp) REVERT: B 726 ASP cc_start: 0.7203 (m-30) cc_final: 0.6954 (m-30) REVERT: B 728 LYS cc_start: 0.7958 (pttt) cc_final: 0.7729 (ptpt) REVERT: B 751 MET cc_start: 0.7950 (mmm) cc_final: 0.7297 (mmm) REVERT: B 810 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7542 (tt) REVERT: B 817 PRO cc_start: 0.8023 (Cg_exo) cc_final: 0.7783 (Cg_endo) REVERT: B 865 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6614 (p0) REVERT: B 923 MET cc_start: 0.6644 (tmm) cc_final: 0.6290 (tmm) REVERT: B 1000 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7490 (mmtm) REVERT: B 1027 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6818 (mmtm) REVERT: B 1120 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7195 (p0) REVERT: B 1132 GLU cc_start: 0.7140 (pp20) cc_final: 0.6780 (pt0) REVERT: B 1143 LYS cc_start: 0.6958 (mttm) cc_final: 0.6617 (mttm) REVERT: B 1147 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7249 (mm-30) REVERT: B 1255 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 1305 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 1323 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7709 (ptt180) REVERT: B 1416 VAL cc_start: 0.8516 (m) cc_final: 0.8106 (p) REVERT: G 13 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8024 (mp) REVERT: G 30 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: G 48 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8296 (mmmm) REVERT: G 55 LYS cc_start: 0.8234 (mptt) cc_final: 0.7979 (mttt) REVERT: G 130 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7361 (ttmm) REVERT: H 18 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: H 25 GLN cc_start: 0.8123 (tt0) cc_final: 0.7815 (tt0) REVERT: H 93 TYR cc_start: 0.8222 (m-80) cc_final: 0.6539 (m-80) REVERT: H 126 ASP cc_start: 0.8619 (t0) cc_final: 0.7983 (t70) REVERT: H 128 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8157 (mtmm) outliers start: 55 outliers final: 37 residues processed: 426 average time/residue: 0.5068 time to fit residues: 327.4769 Evaluate side-chains 441 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 394 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 181 HIS 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 1175 VAL 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 90 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 354 ARG 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 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 550 LYS Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU 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 1025 SER 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 B residue 1403 THR Chi-restraints excluded: chain B residue 1423 LEU 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 71 GLU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 104 optimal weight: 0.5980 chunk 200 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 98 optimal weight: 0.2980 chunk 171 optimal weight: 0.0010 chunk 8 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 chunk 84 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.220225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167890 restraints weight = 46824.149| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.87 r_work: 0.3710 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31440 Z= 0.118 Angle : 0.548 9.897 43654 Z= 0.294 Chirality : 0.039 0.178 4937 Planarity : 0.003 0.040 4540 Dihedral : 20.128 178.063 7088 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.52 % Allowed : 16.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2913 helix: 1.16 (0.15), residues: 1206 sheet: -0.22 (0.27), residues: 342 loop : -0.91 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B1005 HIS 0.013 0.001 HIS B1108 PHE 0.030 0.001 PHE A 708 TYR 0.017 0.001 TYR A1239 ARG 0.005 0.000 ARG B1408 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1250) hydrogen bonds : angle 4.02573 ( 3290) covalent geometry : bond 0.00254 (31440) covalent geometry : angle 0.54810 (43654) *********************** 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 440 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 399 time to evaluate : 2.692 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: A 13 ASN cc_start: 0.8504 (p0) cc_final: 0.8082 (p0) REVERT: A 113 GLU cc_start: 0.6294 (tp30) cc_final: 0.5998 (tp30) REVERT: A 171 GLU cc_start: 0.6987 (mm-30) cc_final: 0.5207 (mt-10) REVERT: A 186 TYR cc_start: 0.7105 (t80) cc_final: 0.6787 (t80) REVERT: A 297 TYR cc_start: 0.4997 (t80) cc_final: 0.4588 (t80) REVERT: A 303 ASN cc_start: 0.7272 (t0) cc_final: 0.6601 (p0) REVERT: A 309 LYS cc_start: 0.7631 (pttp) cc_final: 0.7342 (ptmt) REVERT: A 317 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 328 ILE cc_start: 0.7271 (pt) cc_final: 0.6992 (mt) REVERT: A 333 LYS cc_start: 0.7884 (tptp) cc_final: 0.7542 (tppt) REVERT: A 366 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6210 (mppt) REVERT: A 380 GLN cc_start: 0.7748 (tt0) cc_final: 0.7525 (tt0) REVERT: A 684 GLU cc_start: 0.7427 (pt0) cc_final: 0.7172 (tt0) REVERT: A 993 MET cc_start: 0.6735 (tpt) cc_final: 0.5765 (tpt) REVERT: A 995 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 1011 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7974 (ptpt) REVERT: A 1099 TRP cc_start: 0.6617 (p90) cc_final: 0.6387 (p90) REVERT: A 1211 ASN cc_start: 0.7453 (m110) cc_final: 0.6928 (m110) REVERT: A 1356 LYS cc_start: 0.7596 (mmtp) cc_final: 0.7307 (mtpp) REVERT: A 1376 GLN cc_start: 0.8059 (pp30) cc_final: 0.7792 (pp30) REVERT: A 1436 GLN cc_start: 0.6024 (tp-100) cc_final: 0.5651 (tp-100) REVERT: B 168 GLU cc_start: 0.7707 (tp30) cc_final: 0.7266 (tt0) REVERT: B 201 PHE cc_start: 0.7906 (t80) cc_final: 0.7706 (t80) REVERT: B 298 GLU cc_start: 0.6422 (mp0) cc_final: 0.5893 (mp0) REVERT: B 323 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 326 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7610 (ttm-80) REVERT: B 330 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 347 ASP cc_start: 0.6352 (m-30) cc_final: 0.6134 (m-30) REVERT: B 374 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 383 LEU cc_start: 0.7955 (mm) cc_final: 0.7589 (mp) REVERT: B 476 LYS cc_start: 0.8525 (mttm) cc_final: 0.8140 (mttm) REVERT: B 499 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7307 (mm-30) REVERT: B 568 PHE cc_start: 0.8235 (m-10) cc_final: 0.7977 (m-10) REVERT: B 571 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6833 (mt-10) REVERT: B 656 MET cc_start: 0.7005 (mpp) cc_final: 0.6667 (mpp) REVERT: B 726 ASP cc_start: 0.7059 (m-30) cc_final: 0.6823 (m-30) REVERT: B 751 MET cc_start: 0.7913 (mmm) cc_final: 0.7273 (mmm) REVERT: B 810 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7584 (tt) REVERT: B 817 PRO cc_start: 0.8055 (Cg_exo) cc_final: 0.7797 (Cg_endo) REVERT: B 865 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6589 (p0) REVERT: B 923 MET cc_start: 0.6683 (tmm) cc_final: 0.6360 (tmm) REVERT: B 1000 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7301 (mmtm) REVERT: B 1143 LYS cc_start: 0.6869 (mttm) cc_final: 0.6332 (mttm) REVERT: B 1147 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6921 (mm-30) REVERT: B 1255 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 1305 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 1309 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7101 (mt0) REVERT: B 1323 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7565 (ptt180) REVERT: B 1440 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7212 (mt-10) REVERT: G 13 LEU cc_start: 0.8320 (mm) cc_final: 0.8028 (mp) REVERT: G 30 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: G 55 LYS cc_start: 0.8183 (mptt) cc_final: 0.7944 (mttt) REVERT: H 18 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: H 25 GLN cc_start: 0.7868 (tt0) cc_final: 0.7533 (tt0) REVERT: H 62 THR cc_start: 0.8542 (t) cc_final: 0.8291 (p) REVERT: H 126 ASP cc_start: 0.8548 (t0) cc_final: 0.7762 (t0) REVERT: H 128 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8169 (mtmm) outliers start: 41 outliers final: 27 residues processed: 422 average time/residue: 0.4771 time to fit residues: 309.2953 Evaluate side-chains 417 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 386 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 1175 VAL 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 192 ASP Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU 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 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 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 71 GLU 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 39 optimal weight: 30.0000 chunk 221 optimal weight: 0.0870 chunk 167 optimal weight: 2.9990 chunk 187 optimal weight: 0.1980 chunk 308 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 340 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 710 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 ASN B 974 GLN B1108 HIS B1120 ASN B1427 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.219022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166527 restraints weight = 46598.485| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.74 r_work: 0.3689 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 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 = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31440 Z= 0.140 Angle : 0.560 9.640 43654 Z= 0.300 Chirality : 0.039 0.175 4937 Planarity : 0.003 0.040 4540 Dihedral : 20.105 177.620 7086 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.37 % Allowed : 16.88 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2913 helix: 1.21 (0.15), residues: 1206 sheet: -0.20 (0.27), residues: 342 loop : -0.89 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 PHE 0.019 0.001 PHE G 88 TYR 0.019 0.001 TYR A 353 ARG 0.005 0.000 ARG B1408 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 1250) hydrogen bonds : angle 4.02023 ( 3290) covalent geometry : bond 0.00308 (31440) covalent geometry : angle 0.56043 (43654) ********************** 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 432 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 395 time to evaluate : 3.676 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: A 13 ASN cc_start: 0.8455 (p0) cc_final: 0.8027 (p0) REVERT: A 113 GLU cc_start: 0.6285 (tp30) cc_final: 0.5997 (tp30) REVERT: A 171 GLU cc_start: 0.7018 (mm-30) cc_final: 0.5203 (mt-10) REVERT: A 181 HIS cc_start: 0.7435 (t-90) cc_final: 0.7199 (m-70) REVERT: A 186 TYR cc_start: 0.7122 (t80) cc_final: 0.6772 (t80) REVERT: A 297 TYR cc_start: 0.5015 (t80) cc_final: 0.4575 (t80) REVERT: A 301 LEU cc_start: 0.8549 (mt) cc_final: 0.8344 (mp) REVERT: A 303 ASN cc_start: 0.7272 (t0) cc_final: 0.6595 (p0) REVERT: A 309 LYS cc_start: 0.7578 (pttp) cc_final: 0.7212 (ptpt) REVERT: A 317 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 328 ILE cc_start: 0.7266 (pt) cc_final: 0.6970 (mt) REVERT: A 333 LYS cc_start: 0.7804 (tptp) cc_final: 0.7449 (tppt) REVERT: A 366 LYS cc_start: 0.7156 (mmmt) cc_final: 0.6103 (mppt) REVERT: A 380 GLN cc_start: 0.7546 (tt0) cc_final: 0.7307 (tt0) REVERT: A 688 THR cc_start: 0.7649 (m) cc_final: 0.7364 (p) REVERT: A 993 MET cc_start: 0.6785 (tpt) cc_final: 0.5987 (tpt) REVERT: A 995 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 997 THR cc_start: 0.7392 (m) cc_final: 0.6833 (t) REVERT: A 1011 LYS cc_start: 0.8518 (ptpt) cc_final: 0.8071 (ptpt) REVERT: A 1099 TRP cc_start: 0.6680 (p90) cc_final: 0.6441 (p90) REVERT: A 1177 LYS cc_start: 0.7624 (ptpp) cc_final: 0.7384 (ptpp) REVERT: A 1211 ASN cc_start: 0.7477 (m110) cc_final: 0.6944 (m110) REVERT: A 1356 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7379 (mtpp) REVERT: A 1376 GLN cc_start: 0.8098 (pp30) cc_final: 0.7657 (pp30) REVERT: A 1431 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7780 (ttmm) REVERT: A 1436 GLN cc_start: 0.6067 (tp-100) cc_final: 0.5634 (tp-100) REVERT: B 168 GLU cc_start: 0.7708 (tp30) cc_final: 0.7233 (tt0) REVERT: B 298 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5897 (mp0) REVERT: B 323 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 326 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7705 (ttm-80) REVERT: B 347 ASP cc_start: 0.6403 (m-30) cc_final: 0.6175 (m-30) REVERT: B 374 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 383 LEU cc_start: 0.7949 (mm) cc_final: 0.7574 (mp) REVERT: B 429 GLN cc_start: 0.8000 (mm110) cc_final: 0.7718 (mm-40) REVERT: B 476 LYS cc_start: 0.8557 (mttm) cc_final: 0.8134 (mttm) REVERT: B 499 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 545 LYS cc_start: 0.8005 (mptt) cc_final: 0.7539 (mmmt) REVERT: B 568 PHE cc_start: 0.8232 (m-10) cc_final: 0.7976 (m-10) REVERT: B 571 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6837 (mt-10) REVERT: B 656 MET cc_start: 0.7061 (mpp) cc_final: 0.6740 (mpp) REVERT: B 726 ASP cc_start: 0.7118 (m-30) cc_final: 0.6856 (m-30) REVERT: B 751 MET cc_start: 0.7957 (mmm) cc_final: 0.7305 (mmm) REVERT: B 810 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 817 PRO cc_start: 0.8115 (Cg_exo) cc_final: 0.7862 (Cg_endo) REVERT: B 865 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6539 (p0) REVERT: B 923 MET cc_start: 0.6779 (tmm) cc_final: 0.6425 (tmm) REVERT: B 943 SER cc_start: 0.7991 (m) cc_final: 0.7773 (t) REVERT: B 994 ASN cc_start: 0.7325 (m-40) cc_final: 0.6977 (m-40) REVERT: B 1000 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7120 (mmtm) REVERT: B 1027 LYS cc_start: 0.7349 (mmtt) cc_final: 0.7076 (mmtt) REVERT: B 1132 GLU cc_start: 0.7066 (pp20) cc_final: 0.6708 (pt0) REVERT: B 1143 LYS cc_start: 0.6855 (mttm) cc_final: 0.6544 (mttm) REVERT: B 1255 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 1305 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 1309 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7196 (mt0) REVERT: B 1323 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7640 (ptt180) REVERT: B 1440 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7188 (mt-10) REVERT: G 13 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8006 (mp) REVERT: G 30 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6115 (pm20) REVERT: G 55 LYS cc_start: 0.8199 (mptt) cc_final: 0.7950 (mttt) REVERT: G 56 MET cc_start: 0.8066 (ppp) cc_final: 0.7848 (ppp) REVERT: G 87 GLN cc_start: 0.8049 (tt0) cc_final: 0.7622 (tt0) REVERT: H 18 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: H 25 GLN cc_start: 0.8009 (tt0) cc_final: 0.7705 (tt0) REVERT: H 62 THR cc_start: 0.8501 (t) cc_final: 0.8244 (p) REVERT: H 126 ASP cc_start: 0.8566 (t0) cc_final: 0.7770 (t0) REVERT: H 128 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8147 (mtmm) outliers start: 37 outliers final: 29 residues processed: 414 average time/residue: 0.6907 time to fit residues: 444.1210 Evaluate side-chains 428 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 393 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1430 THR 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 354 ARG Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 729 LYS Chi-restraints excluded: chain B residue 738 GLU 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 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 67 LYS Chi-restraints excluded: chain G residue 71 GLU 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 211 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 50.0000 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN B 410 GLN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 GLN B1427 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.217547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164576 restraints weight = 46567.441| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.76 r_work: 0.3663 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 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 = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31440 Z= 0.196 Angle : 0.594 9.695 43654 Z= 0.318 Chirality : 0.041 0.180 4937 Planarity : 0.004 0.053 4540 Dihedral : 20.154 177.258 7086 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.41 % Allowed : 17.02 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 2913 helix: 1.11 (0.15), residues: 1207 sheet: -0.20 (0.27), residues: 342 loop : -0.94 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1005 HIS 0.013 0.001 HIS B1108 PHE 0.019 0.001 PHE G 88 TYR 0.021 0.001 TYR A 353 ARG 0.005 0.000 ARG B1408 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 1250) hydrogen bonds : angle 4.10828 ( 3290) covalent geometry : bond 0.00434 (31440) covalent geometry : angle 0.59433 (43654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22996.84 seconds wall clock time: 403 minutes 8.96 seconds (24188.96 seconds total)