Starting phenix.real_space_refine on Thu Jul 25 20:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_37762_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_37762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_37762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_37762_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wr4_37762/07_2024/8wr4_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 Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 1147": "OE1" <-> "OE2" Residue "B GLU 1317": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 21.34, per 1000 atoms: 0.71 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.13 Conformation dependent library (CDL) restraints added in 5.7 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: 10.80 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: 16.72 Time building geometry restraints manager: 14.21 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: 97.55 - 104.84: 1402 104.84 - 112.14: 16042 112.14 - 119.43: 10701 119.43 - 126.73: 14473 126.73 - 134.02: 1036 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 2.520 nonbonded pdb=" O2 U N 35 " pdb=" N4 C N 36 " model vdw 2.156 2.520 nonbonded pdb=" O2' A N 11 " pdb=" O4' A N 12 " model vdw 2.174 2.440 nonbonded pdb=" O ILE H 82 " pdb=" OG SER H 86 " model vdw 2.197 2.440 ... (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 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 96.960 Find NCS groups from input model: 0.420 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.200 ------------------------------------------------------------------------------- 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= 0.230 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 488 time to evaluate : 2.930 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: 0.4731 time to fit residues: 354.0973 Evaluate side-chains 427 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 423 time to evaluate : 2.910 ------------------------------------------------------------------------------- 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: 0.7980 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 0.0980 chunk 185 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 944 ASN B 974 GLN G 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1242 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= 0.204 Angle : 0.542 8.727 43654 Z= 0.292 Chirality : 0.040 0.197 4937 Planarity : 0.003 0.046 4540 Dihedral : 20.333 179.948 7097 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.15 % Allowed : 7.62 % Favored : 91.23 % 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: 1193 sheet: -0.38 (0.27), residues: 351 loop : -0.86 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1005 HIS 0.008 0.001 HIS A 287 PHE 0.030 0.001 PHE B 871 TYR 0.024 0.001 TYR A 345 ARG 0.006 0.000 ARG A1028 *********************** 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 468 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 437 time to evaluate : 2.954 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: 0.7025 (p90) cc_final: 0.6704 (p90) REVERT: A 113 GLU cc_start: 0.7587 (tt0) cc_final: 0.7197 (tp30) REVERT: A 134 ASN cc_start: 0.8099 (m110) cc_final: 0.7739 (m110) REVERT: A 135 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7567 (tp30) REVERT: A 136 MET cc_start: 0.7651 (tmm) cc_final: 0.7390 (tmm) REVERT: A 186 TYR cc_start: 0.7010 (t80) cc_final: 0.6315 (t80) REVERT: A 309 LYS cc_start: 0.7307 (pttp) cc_final: 0.7025 (ptpt) REVERT: A 317 GLU cc_start: 0.7765 (mm-30) cc_final: 0.6828 (mp0) REVERT: A 334 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7638 (pt0) REVERT: A 335 PHE cc_start: 0.7970 (m-80) cc_final: 0.7690 (m-10) REVERT: A 696 ASP cc_start: 0.7782 (t0) cc_final: 0.7280 (t0) REVERT: A 706 LYS cc_start: 0.7945 (pttm) cc_final: 0.7665 (ptpp) REVERT: A 708 PHE cc_start: 0.7984 (t80) cc_final: 0.7779 (t80) REVERT: A 710 ASN cc_start: 0.7229 (m-40) cc_final: 0.6660 (m-40) REVERT: A 713 HIS cc_start: 0.6307 (m-70) cc_final: 0.5991 (m-70) REVERT: A 993 MET cc_start: 0.6753 (tpt) cc_final: 0.5701 (tpt) REVERT: A 995 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7199 (tm-30) REVERT: A 1011 LYS cc_start: 0.8491 (ptpt) cc_final: 0.8146 (ptpt) REVERT: A 1029 ILE cc_start: 0.8401 (pt) cc_final: 0.8168 (pt) REVERT: A 1185 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7192 (mtp180) REVERT: A 1187 SER cc_start: 0.8189 (m) cc_final: 0.7781 (p) REVERT: A 1239 TYR cc_start: 0.7741 (m-80) cc_final: 0.7540 (m-80) REVERT: A 1250 LYS cc_start: 0.7793 (mttt) cc_final: 0.6859 (mttt) REVERT: A 1302 GLU cc_start: 0.7719 (tt0) cc_final: 0.7260 (tt0) REVERT: A 1305 GLU cc_start: 0.7757 (tp30) cc_final: 0.7086 (tm-30) REVERT: A 1323 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7660 (ttp80) REVERT: A 1436 GLN cc_start: 0.6233 (tp-100) cc_final: 0.5550 (tp-100) REVERT: B 102 GLU cc_start: 0.7488 (mp0) cc_final: 0.7209 (mp0) REVERT: B 103 LYS cc_start: 0.7385 (tptm) cc_final: 0.7110 (tptm) REVERT: B 166 LYS cc_start: 0.8110 (tttt) cc_final: 0.7859 (tttt) REVERT: B 168 GLU cc_start: 0.7643 (tp30) cc_final: 0.6987 (tt0) REVERT: B 169 LYS cc_start: 0.7834 (ptpt) cc_final: 0.7466 (ptpt) REVERT: B 201 PHE cc_start: 0.7807 (t80) cc_final: 0.7566 (t80) REVERT: B 282 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 298 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: B 324 GLU cc_start: 0.7925 (tt0) cc_final: 0.7684 (tt0) REVERT: B 326 ARG cc_start: 0.7651 (tpp80) cc_final: 0.7242 (ttm110) REVERT: B 365 LYS cc_start: 0.7223 (mmpt) cc_final: 0.6947 (mmpt) REVERT: B 383 LEU cc_start: 0.7598 (mm) cc_final: 0.7321 (mp) REVERT: B 476 LYS cc_start: 0.8768 (mttm) cc_final: 0.8308 (mttm) REVERT: B 497 CYS cc_start: 0.8060 (m) cc_final: 0.7859 (m) REVERT: B 564 LYS cc_start: 0.8568 (mttt) cc_final: 0.8019 (mttt) REVERT: B 591 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8490 (tmtt) REVERT: B 710 ASN cc_start: 0.7249 (m110) cc_final: 0.6901 (m110) REVERT: B 726 ASP cc_start: 0.7406 (m-30) cc_final: 0.6863 (m-30) REVERT: B 728 LYS cc_start: 0.7638 (pttm) cc_final: 0.7073 (pttt) REVERT: B 729 LYS cc_start: 0.7818 (ptmm) cc_final: 0.7451 (pttp) REVERT: B 733 GLN cc_start: 0.7397 (mp10) cc_final: 0.7177 (mp10) REVERT: B 751 MET cc_start: 0.8098 (mmm) cc_final: 0.7711 (mmm) REVERT: B 881 GLU cc_start: 0.8350 (tt0) cc_final: 0.7853 (tm-30) REVERT: B 923 MET cc_start: 0.6657 (tmm) cc_final: 0.5927 (tmm) REVERT: B 1022 LYS cc_start: 0.8211 (tttp) cc_final: 0.7800 (tptp) REVERT: B 1027 LYS cc_start: 0.6774 (mmmt) cc_final: 0.6472 (mmtt) REVERT: B 1107 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7956 (tttp) REVERT: B 1108 HIS cc_start: 0.6304 (m170) cc_final: 0.5979 (m170) REVERT: B 1116 SER cc_start: 0.8539 (t) cc_final: 0.8224 (p) REVERT: B 1120 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7178 (p0) REVERT: B 1133 LYS cc_start: 0.6399 (ptmt) cc_final: 0.6190 (ttpp) REVERT: B 1143 LYS cc_start: 0.7220 (mttt) cc_final: 0.6910 (mttm) REVERT: B 1144 GLU cc_start: 0.7264 (tp30) cc_final: 0.6825 (tp30) REVERT: B 1147 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 1211 ASN cc_start: 0.7041 (m-40) cc_final: 0.6670 (m-40) REVERT: B 1219 ASN cc_start: 0.7497 (t0) cc_final: 0.7166 (t0) REVERT: B 1255 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 1269 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7990 (ptpt) REVERT: B 1305 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 1323 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7282 (ptt180) REVERT: B 1354 LYS cc_start: 0.7501 (ttpt) cc_final: 0.7242 (tptp) REVERT: B 1370 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6425 (mm-30) REVERT: B 1416 VAL cc_start: 0.8036 (m) cc_final: 0.7722 (p) REVERT: B 1426 ILE cc_start: 0.8270 (mm) cc_final: 0.8032 (mp) REVERT: G 13 LEU cc_start: 0.7542 (mm) cc_final: 0.7287 (mp) REVERT: G 30 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6494 (pm20) REVERT: G 48 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7911 (mmmm) REVERT: G 56 MET cc_start: 0.7790 (tmm) cc_final: 0.7328 (ppp) REVERT: G 76 LEU cc_start: 0.8194 (mt) cc_final: 0.7973 (mm) REVERT: G 94 ASN cc_start: 0.7207 (t0) cc_final: 0.6936 (t0) REVERT: H 25 GLN cc_start: 0.7886 (tt0) cc_final: 0.7543 (tt0) REVERT: H 34 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7309 (mmmt) REVERT: H 59 LYS cc_start: 0.7680 (mttp) cc_final: 0.7353 (tppp) REVERT: H 126 ASP cc_start: 0.8291 (t0) cc_final: 0.7619 (t70) REVERT: H 128 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7589 (mtmm) outliers start: 31 outliers final: 18 residues processed: 448 average time/residue: 0.4852 time to fit residues: 328.9574 Evaluate side-chains 440 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 419 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN 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 B residue 12 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1097 LYS Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1301 ASN 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 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 240 optimal weight: 0.0870 chunk 196 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 651 HIS A 685 GLN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 675 GLN B 960 ASN B 974 GLN B1033 HIS B1235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31440 Z= 0.302 Angle : 0.575 9.066 43654 Z= 0.310 Chirality : 0.042 0.217 4937 Planarity : 0.004 0.044 4540 Dihedral : 20.298 179.641 7092 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.67 % Allowed : 10.33 % Favored : 88.01 % 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: -0.07 (0.15), residues: 2913 helix: 1.10 (0.15), residues: 1189 sheet: -0.38 (0.27), residues: 343 loop : -0.95 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1005 HIS 0.009 0.001 HIS B1033 PHE 0.019 0.002 PHE A 49 TYR 0.018 0.001 TYR A 345 ARG 0.007 0.001 ARG A 71 *********************** 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 484 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 439 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6385 (tm-30) REVERT: A 113 GLU cc_start: 0.7667 (tt0) cc_final: 0.7152 (tp30) REVERT: A 127 PHE cc_start: 0.6729 (t80) cc_final: 0.6284 (t80) REVERT: A 134 ASN cc_start: 0.8084 (m110) cc_final: 0.7721 (m110) REVERT: A 135 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7683 (tp30) REVERT: A 136 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7366 (tmm) REVERT: A 304 PRO cc_start: 0.8356 (Cg_endo) cc_final: 0.8149 (Cg_exo) REVERT: A 328 ILE cc_start: 0.6791 (pt) cc_final: 0.6534 (mt) REVERT: A 333 LYS cc_start: 0.7704 (tttp) cc_final: 0.7333 (tptp) REVERT: A 334 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7756 (pt0) REVERT: A 336 HIS cc_start: 0.7246 (m-70) cc_final: 0.7027 (m170) REVERT: A 696 ASP cc_start: 0.7887 (t0) cc_final: 0.7385 (t0) REVERT: A 710 ASN cc_start: 0.7106 (m-40) cc_final: 0.6491 (m-40) REVERT: A 936 LYS cc_start: 0.7681 (pttt) cc_final: 0.7481 (pttt) REVERT: A 993 MET cc_start: 0.6834 (tpt) cc_final: 0.5779 (tpt) REVERT: A 995 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 1011 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8157 (ptpt) REVERT: A 1029 ILE cc_start: 0.8539 (pt) cc_final: 0.8274 (pt) REVERT: A 1099 TRP cc_start: 0.6922 (p90) cc_final: 0.6220 (p90) REVERT: A 1102 PHE cc_start: 0.6988 (t80) cc_final: 0.6722 (t80) REVERT: A 1172 TRP cc_start: 0.8262 (p90) cc_final: 0.7829 (p90) REVERT: A 1185 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7298 (mtp180) REVERT: A 1187 SER cc_start: 0.8321 (m) cc_final: 0.7939 (p) REVERT: A 1238 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7336 (ttpp) REVERT: A 1250 LYS cc_start: 0.7654 (mttt) cc_final: 0.6780 (mtmt) REVERT: A 1302 GLU cc_start: 0.7674 (tt0) cc_final: 0.7251 (tt0) REVERT: A 1305 GLU cc_start: 0.7770 (tp30) cc_final: 0.7339 (tp30) REVERT: A 1309 GLN cc_start: 0.7710 (mm110) cc_final: 0.7283 (mm-40) REVERT: A 1325 LEU cc_start: 0.7819 (mm) cc_final: 0.7562 (mp) REVERT: A 1376 GLN cc_start: 0.7962 (pp30) cc_final: 0.7345 (pp30) REVERT: A 1390 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7506 (mtpt) REVERT: A 1412 THR cc_start: 0.7407 (p) cc_final: 0.7190 (p) REVERT: A 1436 GLN cc_start: 0.6256 (tp-100) cc_final: 0.5641 (tp-100) REVERT: B 102 GLU cc_start: 0.7485 (mp0) cc_final: 0.6928 (pm20) REVERT: B 103 LYS cc_start: 0.7462 (tptm) cc_final: 0.7206 (tptm) REVERT: B 166 LYS cc_start: 0.8169 (tttt) cc_final: 0.7935 (tttt) REVERT: B 168 GLU cc_start: 0.7626 (tp30) cc_final: 0.7003 (tt0) REVERT: B 169 LYS cc_start: 0.7918 (ptpt) cc_final: 0.7532 (ptpt) REVERT: B 201 PHE cc_start: 0.7762 (t80) cc_final: 0.7545 (t80) REVERT: B 290 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7577 (mtmm) REVERT: B 298 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: B 309 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8325 (mmmm) REVERT: B 324 GLU cc_start: 0.7990 (tt0) cc_final: 0.7758 (tt0) REVERT: B 326 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7282 (ttm110) REVERT: B 343 ASP cc_start: 0.6592 (p0) cc_final: 0.6158 (p0) REVERT: B 347 ASP cc_start: 0.6572 (m-30) cc_final: 0.6163 (m-30) REVERT: B 365 LYS cc_start: 0.7260 (mmpt) cc_final: 0.6989 (mmpt) REVERT: B 476 LYS cc_start: 0.8754 (mttm) cc_final: 0.8290 (mttm) REVERT: B 497 CYS cc_start: 0.7849 (m) cc_final: 0.7321 (m) REVERT: B 564 LYS cc_start: 0.8636 (mttt) cc_final: 0.8135 (mttt) REVERT: B 591 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8597 (tmtt) REVERT: B 593 TRP cc_start: 0.6323 (t60) cc_final: 0.5989 (t60) REVERT: B 684 GLU cc_start: 0.7452 (pt0) cc_final: 0.7240 (tt0) REVERT: B 710 ASN cc_start: 0.7191 (m110) cc_final: 0.6726 (m110) REVERT: B 726 ASP cc_start: 0.7340 (m-30) cc_final: 0.6772 (m-30) REVERT: B 728 LYS cc_start: 0.7854 (pttm) cc_final: 0.7304 (pmtt) REVERT: B 751 MET cc_start: 0.8166 (mmm) cc_final: 0.7739 (mmm) REVERT: B 995 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7181 (tm-30) REVERT: B 1022 LYS cc_start: 0.8298 (tttp) cc_final: 0.7834 (tptp) REVERT: B 1025 SER cc_start: 0.7476 (t) cc_final: 0.7144 (t) REVERT: B 1027 LYS cc_start: 0.6961 (mmmt) cc_final: 0.6368 (mmtm) REVERT: B 1107 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7870 (tttp) REVERT: B 1108 HIS cc_start: 0.6510 (m170) cc_final: 0.6191 (m170) REVERT: B 1116 SER cc_start: 0.8504 (t) cc_final: 0.8274 (p) REVERT: B 1120 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 1133 LYS cc_start: 0.6712 (ptmt) cc_final: 0.6450 (ttpp) REVERT: B 1144 GLU cc_start: 0.7233 (tp30) cc_final: 0.6871 (tp30) REVERT: B 1219 ASN cc_start: 0.7721 (t0) cc_final: 0.7322 (t0) REVERT: B 1255 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7236 (mm-30) REVERT: B 1305 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 1323 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7162 (ptt180) REVERT: B 1354 LYS cc_start: 0.7500 (ttpt) cc_final: 0.7218 (tptp) REVERT: B 1355 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: B 1370 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6580 (mm-30) REVERT: B 1416 VAL cc_start: 0.8088 (m) cc_final: 0.7804 (p) REVERT: B 1426 ILE cc_start: 0.8277 (mm) cc_final: 0.8061 (mp) REVERT: B 1427 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6688 (t0) REVERT: G 5 LYS cc_start: 0.7076 (mtpp) cc_final: 0.6554 (mtpp) REVERT: G 13 LEU cc_start: 0.7573 (mm) cc_final: 0.7326 (mp) REVERT: G 30 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: G 48 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7925 (mmmm) REVERT: G 56 MET cc_start: 0.7793 (tmm) cc_final: 0.7492 (tmm) REVERT: G 76 LEU cc_start: 0.8298 (mt) cc_final: 0.8098 (mm) REVERT: G 112 THR cc_start: 0.8027 (m) cc_final: 0.7672 (p) REVERT: H 9 ASP cc_start: 0.7535 (t0) cc_final: 0.7126 (t0) REVERT: H 18 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: H 25 GLN cc_start: 0.8074 (tt0) cc_final: 0.7664 (tt0) REVERT: H 57 ASP cc_start: 0.6491 (t0) cc_final: 0.6160 (m-30) REVERT: H 59 LYS cc_start: 0.7660 (mttp) cc_final: 0.7056 (tppp) REVERT: H 62 THR cc_start: 0.7988 (m) cc_final: 0.7593 (t) REVERT: H 93 TYR cc_start: 0.8060 (m-80) cc_final: 0.6459 (m-80) REVERT: H 119 MET cc_start: 0.7801 (mmm) cc_final: 0.7517 (mtp) REVERT: H 128 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7505 (mtmm) outliers start: 45 outliers final: 22 residues processed: 460 average time/residue: 0.5226 time to fit residues: 368.4690 Evaluate side-chains 442 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 412 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 157 HIS 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 1114 ILE Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1001 ASP 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 1301 ASN Chi-restraints excluded: chain B residue 1355 GLU 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 104 SER Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 194 optimal weight: 6.9990 chunk 290 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 685 GLN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** B 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2200 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= 0.182 Angle : 0.515 8.987 43654 Z= 0.278 Chirality : 0.039 0.201 4937 Planarity : 0.003 0.043 4540 Dihedral : 20.215 179.364 7092 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 1.55 % Allowed : 12.73 % Favored : 85.71 % 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: 1.22 (0.15), residues: 1198 sheet: -0.29 (0.28), residues: 343 loop : -0.89 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 PHE 0.022 0.001 PHE G 88 TYR 0.038 0.001 TYR B1064 ARG 0.004 0.000 ARG B1063 *********************** 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 464 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 422 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6410 (tm-30) REVERT: A 113 GLU cc_start: 0.7613 (tt0) cc_final: 0.7122 (tp30) REVERT: A 127 PHE cc_start: 0.6662 (t80) cc_final: 0.6273 (t80) REVERT: A 134 ASN cc_start: 0.8060 (m110) cc_final: 0.7684 (m110) REVERT: A 135 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7683 (tp30) REVERT: A 136 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7448 (tmm) REVERT: A 328 ILE cc_start: 0.6760 (pt) cc_final: 0.6474 (mt) REVERT: A 330 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6378 (mm-30) REVERT: A 334 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7195 (mp0) REVERT: A 696 ASP cc_start: 0.7933 (t0) cc_final: 0.7405 (t0) REVERT: A 706 LYS cc_start: 0.8134 (pttm) cc_final: 0.7779 (ptpp) REVERT: A 993 MET cc_start: 0.6838 (tpt) cc_final: 0.5731 (tpt) REVERT: A 995 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7270 (tm-30) REVERT: A 1011 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8113 (ptpt) REVERT: A 1029 ILE cc_start: 0.8533 (pt) cc_final: 0.8308 (pt) REVERT: A 1037 ASP cc_start: 0.7455 (m-30) cc_final: 0.7074 (m-30) REVERT: A 1099 TRP cc_start: 0.6884 (p90) cc_final: 0.6206 (p90) REVERT: A 1102 PHE cc_start: 0.6942 (t80) cc_final: 0.6564 (t80) REVERT: A 1132 GLU cc_start: 0.6684 (mt-10) cc_final: 0.6352 (mp0) REVERT: A 1172 TRP cc_start: 0.8189 (p90) cc_final: 0.7778 (p90) REVERT: A 1185 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7237 (mtp180) REVERT: A 1187 SER cc_start: 0.8310 (m) cc_final: 0.7923 (p) REVERT: A 1238 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7325 (ttpp) REVERT: A 1250 LYS cc_start: 0.7730 (mttt) cc_final: 0.6750 (mttt) REVERT: A 1302 GLU cc_start: 0.7697 (tt0) cc_final: 0.7258 (tt0) REVERT: A 1305 GLU cc_start: 0.7734 (tp30) cc_final: 0.7355 (tp30) REVERT: A 1309 GLN cc_start: 0.7681 (mm110) cc_final: 0.7333 (mm-40) REVERT: A 1325 LEU cc_start: 0.7786 (mm) cc_final: 0.7519 (mp) REVERT: A 1356 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7224 (mtpp) REVERT: A 1382 ILE cc_start: 0.7786 (mt) cc_final: 0.7530 (mt) REVERT: A 1388 LYS cc_start: 0.8094 (tmmt) cc_final: 0.7845 (ttpp) REVERT: A 1436 GLN cc_start: 0.6184 (tp-100) cc_final: 0.5605 (tp-100) REVERT: B 103 LYS cc_start: 0.7400 (tptm) cc_final: 0.7088 (tptm) REVERT: B 168 GLU cc_start: 0.7612 (tp30) cc_final: 0.7058 (mt-10) REVERT: B 290 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7582 (mtmm) REVERT: B 298 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: B 309 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8283 (mmmm) REVERT: B 324 GLU cc_start: 0.7917 (tt0) cc_final: 0.7698 (tt0) REVERT: B 326 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7256 (ttm110) REVERT: B 343 ASP cc_start: 0.6532 (p0) cc_final: 0.6106 (p0) REVERT: B 347 ASP cc_start: 0.6640 (m-30) cc_final: 0.6231 (m-30) REVERT: B 354 ARG cc_start: 0.7476 (ptp90) cc_final: 0.7257 (ptp90) REVERT: B 365 LYS cc_start: 0.7250 (mmpt) cc_final: 0.7032 (mmpt) REVERT: B 425 PHE cc_start: 0.6328 (m-10) cc_final: 0.6001 (m-10) REVERT: B 476 LYS cc_start: 0.8726 (mttm) cc_final: 0.8253 (mttm) REVERT: B 564 LYS cc_start: 0.8626 (mttt) cc_final: 0.8125 (mttt) REVERT: B 591 LYS cc_start: 0.8794 (tmmt) cc_final: 0.8508 (tmtt) REVERT: B 593 TRP cc_start: 0.6347 (t60) cc_final: 0.5976 (t60) REVERT: B 710 ASN cc_start: 0.7222 (m110) cc_final: 0.6852 (m110) REVERT: B 726 ASP cc_start: 0.7284 (m-30) cc_final: 0.6805 (m-30) REVERT: B 733 GLN cc_start: 0.7515 (mp10) cc_final: 0.7301 (mp10) REVERT: B 751 MET cc_start: 0.8175 (mmm) cc_final: 0.7730 (mmm) REVERT: B 881 GLU cc_start: 0.8340 (tt0) cc_final: 0.7983 (tm-30) REVERT: B 991 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 995 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 1022 LYS cc_start: 0.8215 (tttp) cc_final: 0.7803 (tptp) REVERT: B 1025 SER cc_start: 0.7265 (t) cc_final: 0.7012 (t) REVERT: B 1027 LYS cc_start: 0.6926 (mmmt) cc_final: 0.6492 (mmtt) REVERT: B 1064 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 1107 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7855 (tttp) REVERT: B 1108 HIS cc_start: 0.6427 (m170) cc_final: 0.6061 (m170) REVERT: B 1116 SER cc_start: 0.8522 (t) cc_final: 0.8245 (p) REVERT: B 1120 ASN cc_start: 0.7337 (p0) cc_final: 0.7017 (p0) REVERT: B 1133 LYS cc_start: 0.6671 (ptmt) cc_final: 0.6412 (ttpp) REVERT: B 1144 GLU cc_start: 0.7217 (tp30) cc_final: 0.6866 (tp30) REVERT: B 1147 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6844 (mm-30) REVERT: B 1219 ASN cc_start: 0.7707 (t0) cc_final: 0.7300 (t0) REVERT: B 1255 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 1305 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 1323 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7138 (ptt180) REVERT: B 1354 LYS cc_start: 0.7433 (ttpt) cc_final: 0.7161 (tptp) REVERT: B 1355 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: B 1370 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6574 (mm-30) REVERT: B 1416 VAL cc_start: 0.8082 (m) cc_final: 0.7828 (p) REVERT: B 1426 ILE cc_start: 0.8247 (mm) cc_final: 0.8022 (mp) REVERT: B 1427 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6792 (t0) REVERT: B 1440 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6909 (mt-10) REVERT: G 9 ASP cc_start: 0.6770 (t70) cc_final: 0.6433 (t70) REVERT: G 13 LEU cc_start: 0.7595 (mm) cc_final: 0.7348 (mp) REVERT: G 30 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: G 56 MET cc_start: 0.7746 (tmm) cc_final: 0.7366 (tmm) REVERT: G 73 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7302 (pt) REVERT: G 76 LEU cc_start: 0.8311 (mt) cc_final: 0.8081 (mm) REVERT: G 123 MET cc_start: 0.8103 (tmm) cc_final: 0.6826 (ptm) REVERT: H 25 GLN cc_start: 0.7925 (tt0) cc_final: 0.7471 (tt0) REVERT: H 57 ASP cc_start: 0.6405 (t0) cc_final: 0.6089 (m-30) REVERT: H 59 LYS cc_start: 0.7613 (mttp) cc_final: 0.7018 (tppp) REVERT: H 62 THR cc_start: 0.7926 (m) cc_final: 0.7660 (t) REVERT: H 128 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7522 (mtmm) outliers start: 42 outliers final: 26 residues processed: 446 average time/residue: 0.4928 time to fit residues: 330.5031 Evaluate side-chains 443 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 408 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 685 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1238 LYS Chi-restraints excluded: chain A residue 1301 ASN 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 302 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 678 LEU 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 965 ASN Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1097 LYS 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 1301 ASN Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1427 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 262 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 275 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 685 GLN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 974 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2402 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= 0.205 Angle : 0.517 8.673 43654 Z= 0.279 Chirality : 0.039 0.194 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.176 179.052 7090 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 13.43 % Favored : 84.64 % 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: 0.11 (0.15), residues: 2913 helix: 1.25 (0.15), residues: 1195 sheet: -0.22 (0.28), residues: 343 loop : -0.89 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 PHE 0.027 0.001 PHE A 708 TYR 0.024 0.001 TYR A 379 ARG 0.006 0.000 ARG B1408 *********************** 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 477 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 425 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 HIS cc_start: 0.6892 (p90) cc_final: 0.6590 (p90) REVERT: A 109 LYS cc_start: 0.8502 (mttt) cc_final: 0.8170 (mmtp) REVERT: A 113 GLU cc_start: 0.7622 (tt0) cc_final: 0.6884 (tp30) REVERT: A 134 ASN cc_start: 0.8071 (m110) cc_final: 0.7690 (m110) REVERT: A 135 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7647 (tp30) REVERT: A 317 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 328 ILE cc_start: 0.6751 (pt) cc_final: 0.6467 (mt) REVERT: A 330 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: A 333 LYS cc_start: 0.7747 (tptp) cc_final: 0.7297 (tptp) REVERT: A 334 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7248 (mp0) REVERT: A 379 TYR cc_start: 0.7077 (t80) cc_final: 0.6750 (t80) REVERT: A 696 ASP cc_start: 0.7929 (t0) cc_final: 0.7425 (t0) REVERT: A 993 MET cc_start: 0.6839 (tpt) cc_final: 0.5796 (tpt) REVERT: A 995 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 1011 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8132 (ptpt) REVERT: A 1029 ILE cc_start: 0.8543 (pt) cc_final: 0.8329 (pt) REVERT: A 1033 HIS cc_start: 0.6653 (p-80) cc_final: 0.6362 (p-80) REVERT: A 1037 ASP cc_start: 0.7372 (m-30) cc_final: 0.7077 (m-30) REVERT: A 1099 TRP cc_start: 0.6814 (p90) cc_final: 0.6266 (p90) REVERT: A 1132 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6386 (mp0) REVERT: A 1172 TRP cc_start: 0.8206 (p90) cc_final: 0.7816 (p90) REVERT: A 1185 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7226 (mtp180) REVERT: A 1187 SER cc_start: 0.8318 (m) cc_final: 0.7930 (p) REVERT: A 1211 ASN cc_start: 0.7443 (m110) cc_final: 0.6848 (m110) REVERT: A 1238 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7331 (ttpp) REVERT: A 1250 LYS cc_start: 0.7741 (mttt) cc_final: 0.6711 (mttt) REVERT: A 1302 GLU cc_start: 0.7692 (tt0) cc_final: 0.7256 (tt0) REVERT: A 1305 GLU cc_start: 0.7736 (tp30) cc_final: 0.7350 (tp30) REVERT: A 1309 GLN cc_start: 0.7687 (mm110) cc_final: 0.7338 (mm-40) REVERT: A 1325 LEU cc_start: 0.7792 (mm) cc_final: 0.7505 (mp) REVERT: A 1341 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 1356 LYS cc_start: 0.7641 (mmtp) cc_final: 0.7235 (mtpp) REVERT: A 1388 LYS cc_start: 0.8148 (tmmt) cc_final: 0.7768 (ttpp) REVERT: A 1436 GLN cc_start: 0.6172 (tp-100) cc_final: 0.5599 (tp-100) REVERT: B 102 GLU cc_start: 0.7442 (mp0) cc_final: 0.7148 (mp0) REVERT: B 103 LYS cc_start: 0.7463 (tptm) cc_final: 0.7192 (tptm) REVERT: B 168 GLU cc_start: 0.7624 (tp30) cc_final: 0.7040 (mt-10) REVERT: B 201 PHE cc_start: 0.7910 (t80) cc_final: 0.7637 (t80) REVERT: B 298 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: B 309 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8245 (mmmm) REVERT: B 313 VAL cc_start: 0.8606 (t) cc_final: 0.8323 (p) REVERT: B 324 GLU cc_start: 0.7942 (tt0) cc_final: 0.7730 (tt0) REVERT: B 326 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7259 (ttm110) REVERT: B 340 GLN cc_start: 0.7038 (mt0) cc_final: 0.6830 (mt0) REVERT: B 347 ASP cc_start: 0.6626 (m-30) cc_final: 0.6231 (m-30) REVERT: B 365 LYS cc_start: 0.7263 (mmpt) cc_final: 0.7042 (mmpt) REVERT: B 432 PHE cc_start: 0.8142 (t80) cc_final: 0.7874 (m-80) REVERT: B 476 LYS cc_start: 0.8723 (mttm) cc_final: 0.8255 (mttm) REVERT: B 497 CYS cc_start: 0.7810 (m) cc_final: 0.7416 (m) REVERT: B 564 LYS cc_start: 0.8605 (mttt) cc_final: 0.8103 (mttt) REVERT: B 587 MET cc_start: 0.5968 (mtt) cc_final: 0.5743 (mtt) REVERT: B 591 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8496 (tmtt) REVERT: B 593 TRP cc_start: 0.6432 (t60) cc_final: 0.6166 (t60) REVERT: B 710 ASN cc_start: 0.7231 (m110) cc_final: 0.6756 (m110) REVERT: B 726 ASP cc_start: 0.7369 (m-30) cc_final: 0.6760 (m-30) REVERT: B 728 LYS cc_start: 0.7866 (pttm) cc_final: 0.7407 (pttt) REVERT: B 733 GLN cc_start: 0.7567 (mp10) cc_final: 0.7298 (mp10) REVERT: B 751 MET cc_start: 0.8175 (mmm) cc_final: 0.7638 (mmm) REVERT: B 881 GLU cc_start: 0.8444 (tt0) cc_final: 0.8073 (tm-30) REVERT: B 943 SER cc_start: 0.8088 (m) cc_final: 0.7869 (t) REVERT: B 991 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 995 GLN cc_start: 0.7447 (tm-30) cc_final: 0.7222 (tm-30) REVERT: B 1022 LYS cc_start: 0.8265 (tttp) cc_final: 0.7854 (tptp) REVERT: B 1025 SER cc_start: 0.7384 (t) cc_final: 0.7124 (t) REVERT: B 1027 LYS cc_start: 0.6943 (mmmt) cc_final: 0.6365 (mmtm) REVERT: B 1047 ASP cc_start: 0.6508 (t70) cc_final: 0.6244 (t70) REVERT: B 1064 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7184 (t80) REVERT: B 1070 LEU cc_start: 0.7727 (tt) cc_final: 0.7010 (tp) REVERT: B 1107 LYS cc_start: 0.8234 (ttpt) cc_final: 0.7839 (tttp) REVERT: B 1108 HIS cc_start: 0.6501 (m170) cc_final: 0.6187 (m170) REVERT: B 1116 SER cc_start: 0.8520 (t) cc_final: 0.8259 (p) REVERT: B 1120 ASN cc_start: 0.7368 (p0) cc_final: 0.7038 (p0) REVERT: B 1133 LYS cc_start: 0.6641 (ptmt) cc_final: 0.6366 (ttpp) REVERT: B 1144 GLU cc_start: 0.7192 (tp30) cc_final: 0.6863 (tp30) REVERT: B 1219 ASN cc_start: 0.7731 (t0) cc_final: 0.7307 (t0) REVERT: B 1255 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 1305 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7332 (mm-30) REVERT: B 1323 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7146 (ptt180) REVERT: B 1354 LYS cc_start: 0.7453 (ttpt) cc_final: 0.7173 (tptp) REVERT: B 1355 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: B 1370 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6645 (mm-30) REVERT: B 1416 VAL cc_start: 0.8075 (m) cc_final: 0.7816 (p) REVERT: B 1426 ILE cc_start: 0.8196 (mm) cc_final: 0.7957 (mp) REVERT: B 1427 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.6772 (t0) REVERT: G 6 ILE cc_start: 0.8077 (mm) cc_final: 0.7534 (tt) REVERT: G 9 ASP cc_start: 0.6655 (t70) cc_final: 0.6286 (t70) REVERT: G 30 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: G 71 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7217 (tm-30) REVERT: G 76 LEU cc_start: 0.8332 (mt) cc_final: 0.8098 (mm) REVERT: H 18 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: H 25 GLN cc_start: 0.7953 (tt0) cc_final: 0.7472 (tt0) REVERT: H 57 ASP cc_start: 0.6404 (t0) cc_final: 0.6079 (m-30) REVERT: H 59 LYS cc_start: 0.7612 (mttp) cc_final: 0.7028 (tppp) REVERT: H 62 THR cc_start: 0.7925 (m) cc_final: 0.7581 (t) REVERT: H 128 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7517 (mtmm) outliers start: 52 outliers final: 31 residues processed: 449 average time/residue: 0.4881 time to fit residues: 334.4650 Evaluate side-chains 450 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 411 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 330 GLU 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 1238 LYS Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1301 ASN 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 284 GLU Chi-restraints excluded: chain B residue 298 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 434 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1064 TYR 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 1301 ASN Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1427 ASN 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 H residue 18 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.2980 chunk 276 optimal weight: 0.5980 chunk 60 optimal weight: 50.0000 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 974 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2594 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= 0.200 Angle : 0.511 8.456 43654 Z= 0.276 Chirality : 0.039 0.189 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.144 178.595 7090 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 1.92 % Allowed : 13.92 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.15), residues: 2913 helix: 1.29 (0.15), residues: 1194 sheet: -0.15 (0.28), residues: 342 loop : -0.87 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1005 HIS 0.007 0.001 HIS A 287 PHE 0.026 0.001 PHE G 88 TYR 0.020 0.001 TYR A 379 ARG 0.007 0.000 ARG B1408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 418 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6374 (tm-30) REVERT: A 94 HIS cc_start: 0.6898 (p90) cc_final: 0.6597 (p90) REVERT: A 113 GLU cc_start: 0.7659 (tt0) cc_final: 0.6908 (tp30) REVERT: A 134 ASN cc_start: 0.8025 (m110) cc_final: 0.7652 (m110) REVERT: A 135 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7705 (tp30) REVERT: A 136 MET cc_start: 0.7585 (tmm) cc_final: 0.7330 (tmm) REVERT: A 171 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5270 (mt-10) REVERT: A 317 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 328 ILE cc_start: 0.6758 (pt) cc_final: 0.6497 (mt) REVERT: A 333 LYS cc_start: 0.7636 (tptp) cc_final: 0.6950 (tptp) REVERT: A 379 TYR cc_start: 0.7029 (t80) cc_final: 0.6745 (t80) REVERT: A 696 ASP cc_start: 0.7909 (t0) cc_final: 0.7385 (t0) REVERT: A 993 MET cc_start: 0.6841 (tpt) cc_final: 0.5766 (tpt) REVERT: A 995 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 1011 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8141 (ptpt) REVERT: A 1029 ILE cc_start: 0.8553 (pt) cc_final: 0.8348 (pt) REVERT: A 1033 HIS cc_start: 0.6584 (p-80) cc_final: 0.6262 (p-80) REVERT: A 1037 ASP cc_start: 0.7271 (m-30) cc_final: 0.6974 (m-30) REVERT: A 1099 TRP cc_start: 0.6791 (p90) cc_final: 0.6244 (p90) REVERT: A 1132 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6375 (mp0) REVERT: A 1172 TRP cc_start: 0.8221 (p90) cc_final: 0.7800 (p90) REVERT: A 1187 SER cc_start: 0.8318 (m) cc_final: 0.7944 (p) REVERT: A 1211 ASN cc_start: 0.7471 (m110) cc_final: 0.6873 (m110) REVERT: A 1250 LYS cc_start: 0.7760 (mttt) cc_final: 0.7284 (mtmt) REVERT: A 1302 GLU cc_start: 0.7692 (tt0) cc_final: 0.7259 (tt0) REVERT: A 1305 GLU cc_start: 0.7736 (tp30) cc_final: 0.7434 (tp30) REVERT: A 1309 GLN cc_start: 0.7689 (mm110) cc_final: 0.7475 (mm110) REVERT: A 1325 LEU cc_start: 0.7766 (mm) cc_final: 0.7444 (mp) REVERT: A 1356 LYS cc_start: 0.7469 (mmtp) cc_final: 0.6991 (mtpp) REVERT: A 1388 LYS cc_start: 0.8159 (tmmt) cc_final: 0.7751 (ttpp) REVERT: A 1436 GLN cc_start: 0.6208 (tp-100) cc_final: 0.5657 (tp-100) REVERT: B 89 ASN cc_start: 0.7755 (p0) cc_final: 0.7545 (p0) REVERT: B 102 GLU cc_start: 0.7447 (mp0) cc_final: 0.7136 (mp0) REVERT: B 103 LYS cc_start: 0.7448 (tptm) cc_final: 0.7172 (tptm) REVERT: B 168 GLU cc_start: 0.7608 (tp30) cc_final: 0.7035 (mt-10) REVERT: B 201 PHE cc_start: 0.7748 (t80) cc_final: 0.7523 (t80) REVERT: B 290 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7667 (mmmt) REVERT: B 298 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: B 309 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8221 (mmmm) REVERT: B 313 VAL cc_start: 0.8611 (t) cc_final: 0.8338 (p) REVERT: B 324 GLU cc_start: 0.7947 (tt0) cc_final: 0.7727 (tt0) REVERT: B 326 ARG cc_start: 0.7603 (tpp80) cc_final: 0.7235 (ttm110) REVERT: B 347 ASP cc_start: 0.6620 (m-30) cc_final: 0.6243 (m-30) REVERT: B 365 LYS cc_start: 0.7250 (mmpt) cc_final: 0.7041 (mmpt) REVERT: B 374 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 432 PHE cc_start: 0.8116 (t80) cc_final: 0.7843 (m-80) REVERT: B 476 LYS cc_start: 0.8714 (mttm) cc_final: 0.8235 (mttm) REVERT: B 564 LYS cc_start: 0.8602 (mttt) cc_final: 0.8100 (mttt) REVERT: B 587 MET cc_start: 0.6035 (mtt) cc_final: 0.5813 (mtt) REVERT: B 591 LYS cc_start: 0.8824 (tmmt) cc_final: 0.8522 (tmtt) REVERT: B 710 ASN cc_start: 0.7233 (m110) cc_final: 0.6758 (m110) REVERT: B 726 ASP cc_start: 0.7373 (m-30) cc_final: 0.6828 (m-30) REVERT: B 728 LYS cc_start: 0.7929 (pttm) cc_final: 0.7564 (pttm) REVERT: B 733 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 751 MET cc_start: 0.8172 (mmm) cc_final: 0.7633 (mmm) REVERT: B 775 GLU cc_start: 0.8743 (tp30) cc_final: 0.8154 (mm-30) REVERT: B 881 GLU cc_start: 0.8441 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 991 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 995 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7234 (tm-30) REVERT: B 1022 LYS cc_start: 0.8264 (tttp) cc_final: 0.7843 (tptp) REVERT: B 1027 LYS cc_start: 0.6947 (mmmt) cc_final: 0.6394 (mmtm) REVERT: B 1047 ASP cc_start: 0.6598 (t70) cc_final: 0.6281 (t70) REVERT: B 1064 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7241 (t80) REVERT: B 1070 LEU cc_start: 0.7713 (tt) cc_final: 0.7024 (tp) REVERT: B 1107 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7856 (tttp) REVERT: B 1108 HIS cc_start: 0.6521 (m170) cc_final: 0.6195 (m170) REVERT: B 1116 SER cc_start: 0.8514 (t) cc_final: 0.8261 (p) REVERT: B 1120 ASN cc_start: 0.7324 (p0) cc_final: 0.7014 (p0) REVERT: B 1133 LYS cc_start: 0.6588 (ptmt) cc_final: 0.6294 (ttpp) REVERT: B 1144 GLU cc_start: 0.7150 (tp30) cc_final: 0.6832 (tp30) REVERT: B 1219 ASN cc_start: 0.7732 (t0) cc_final: 0.7324 (t0) REVERT: B 1255 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7246 (mm-30) REVERT: B 1269 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7341 (mtmm) REVERT: B 1305 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 1323 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7141 (ptt180) REVERT: B 1354 LYS cc_start: 0.7462 (ttpt) cc_final: 0.7191 (tptp) REVERT: B 1355 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 1370 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6702 (mm-30) REVERT: B 1416 VAL cc_start: 0.8071 (m) cc_final: 0.7800 (p) REVERT: B 1426 ILE cc_start: 0.8196 (mm) cc_final: 0.7952 (mp) REVERT: B 1427 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6836 (t0) REVERT: G 6 ILE cc_start: 0.8045 (mm) cc_final: 0.7521 (tt) REVERT: G 9 ASP cc_start: 0.6622 (t70) cc_final: 0.6292 (t70) REVERT: G 30 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: G 55 LYS cc_start: 0.8022 (mptt) cc_final: 0.7687 (mttt) REVERT: G 71 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7229 (tm-30) REVERT: G 130 LYS cc_start: 0.7636 (ttmm) cc_final: 0.7359 (ttmm) REVERT: H 9 ASP cc_start: 0.7482 (t0) cc_final: 0.7120 (t0) REVERT: H 18 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: H 25 GLN cc_start: 0.7881 (tt0) cc_final: 0.7374 (tt0) REVERT: H 57 ASP cc_start: 0.6389 (t0) cc_final: 0.6068 (m-30) REVERT: H 59 LYS cc_start: 0.7632 (mttp) cc_final: 0.7012 (tppp) REVERT: H 62 THR cc_start: 0.7879 (m) cc_final: 0.7656 (t) outliers start: 52 outliers final: 36 residues processed: 444 average time/residue: 0.4837 time to fit residues: 325.0276 Evaluate side-chains 453 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 409 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 685 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1301 ASN Chi-restraints excluded: chain B residue 1355 GLU Chi-restraints excluded: chain B residue 1427 ASN 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 82 ILE Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 259 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 340 GLN B 359 HIS B 477 HIS B 974 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31440 Z= 0.312 Angle : 0.567 8.591 43654 Z= 0.305 Chirality : 0.041 0.190 4937 Planarity : 0.004 0.041 4540 Dihedral : 20.200 177.904 7090 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 2.22 % Allowed : 14.40 % Favored : 83.38 % 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: 0.01 (0.15), residues: 2913 helix: 1.14 (0.15), residues: 1189 sheet: -0.15 (0.27), residues: 342 loop : -0.94 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B1005 HIS 0.007 0.001 HIS B 359 PHE 0.025 0.002 PHE G 88 TYR 0.023 0.002 TYR A 186 ARG 0.005 0.000 ARG A 65 *********************** 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 481 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 421 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8002 (p0) cc_final: 0.7589 (p0) REVERT: A 94 HIS cc_start: 0.6915 (p90) cc_final: 0.6654 (p90) REVERT: A 113 GLU cc_start: 0.7773 (tt0) cc_final: 0.6998 (tp30) REVERT: A 127 PHE cc_start: 0.6682 (t80) cc_final: 0.6263 (t80) REVERT: A 134 ASN cc_start: 0.8102 (m110) cc_final: 0.7719 (m110) REVERT: A 135 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7597 (tp30) REVERT: A 156 TYR cc_start: 0.6545 (m-10) cc_final: 0.6328 (m-10) REVERT: A 171 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5076 (mt-10) REVERT: A 317 GLU cc_start: 0.7715 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 328 ILE cc_start: 0.6778 (pt) cc_final: 0.6565 (mt) REVERT: A 333 LYS cc_start: 0.7703 (tptp) cc_final: 0.7050 (tptp) REVERT: A 379 TYR cc_start: 0.7014 (t80) cc_final: 0.6483 (t80) REVERT: A 696 ASP cc_start: 0.7957 (t0) cc_final: 0.7450 (t0) REVERT: A 993 MET cc_start: 0.6905 (tpt) cc_final: 0.5852 (tpt) REVERT: A 995 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 1011 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8188 (ptpt) REVERT: A 1029 ILE cc_start: 0.8550 (pt) cc_final: 0.8339 (pt) REVERT: A 1037 ASP cc_start: 0.7252 (m-30) cc_final: 0.6837 (m-30) REVERT: A 1099 TRP cc_start: 0.6856 (p90) cc_final: 0.6391 (p90) REVERT: A 1172 TRP cc_start: 0.8349 (p90) cc_final: 0.7871 (p90) REVERT: A 1187 SER cc_start: 0.8358 (m) cc_final: 0.7981 (p) REVERT: A 1211 ASN cc_start: 0.7519 (m110) cc_final: 0.6945 (m110) REVERT: A 1250 LYS cc_start: 0.7697 (mttt) cc_final: 0.7313 (mtmt) REVERT: A 1302 GLU cc_start: 0.7719 (tt0) cc_final: 0.7176 (tt0) REVERT: A 1305 GLU cc_start: 0.7715 (tp30) cc_final: 0.7467 (tp30) REVERT: A 1309 GLN cc_start: 0.7702 (mm110) cc_final: 0.7441 (mm-40) REVERT: A 1317 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6680 (mm-30) REVERT: A 1325 LEU cc_start: 0.7829 (mm) cc_final: 0.7504 (mp) REVERT: A 1356 LYS cc_start: 0.7489 (mmtp) cc_final: 0.7071 (mtpp) REVERT: A 1388 LYS cc_start: 0.8213 (tmmt) cc_final: 0.7782 (ttpp) REVERT: A 1436 GLN cc_start: 0.6160 (tp-100) cc_final: 0.5646 (tp-100) REVERT: B 89 ASN cc_start: 0.7822 (p0) cc_final: 0.7504 (p0) REVERT: B 90 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: B 102 GLU cc_start: 0.7461 (mp0) cc_final: 0.7144 (mp0) REVERT: B 103 LYS cc_start: 0.7479 (tptm) cc_final: 0.7202 (tptm) REVERT: B 168 GLU cc_start: 0.7627 (tp30) cc_final: 0.6903 (tt0) REVERT: B 169 LYS cc_start: 0.7907 (ptpt) cc_final: 0.7517 (ptpt) REVERT: B 201 PHE cc_start: 0.7733 (t80) cc_final: 0.7477 (t80) REVERT: B 290 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7853 (mmmt) REVERT: B 298 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: B 309 LYS cc_start: 0.8516 (mmmm) cc_final: 0.8161 (mtpp) REVERT: B 323 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 326 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7273 (ttm110) REVERT: B 347 ASP cc_start: 0.6576 (m-30) cc_final: 0.6205 (m-30) REVERT: B 365 LYS cc_start: 0.7271 (mmpt) cc_final: 0.7037 (mmpt) REVERT: B 374 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7463 (mm-30) REVERT: B 476 LYS cc_start: 0.8716 (mttm) cc_final: 0.8240 (mttm) REVERT: B 497 CYS cc_start: 0.7623 (m) cc_final: 0.6922 (m) REVERT: B 499 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 545 LYS cc_start: 0.7068 (mptt) cc_final: 0.6851 (mmtt) REVERT: B 550 LYS cc_start: 0.7344 (mppt) cc_final: 0.6972 (mppt) REVERT: B 564 LYS cc_start: 0.8660 (mttt) cc_final: 0.8151 (mttt) REVERT: B 571 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6893 (mt-10) REVERT: B 587 MET cc_start: 0.5863 (mtt) cc_final: 0.5626 (mtt) REVERT: B 591 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8530 (tmtt) REVERT: B 710 ASN cc_start: 0.7196 (m110) cc_final: 0.6718 (m110) REVERT: B 719 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7354 (mp0) REVERT: B 726 ASP cc_start: 0.7342 (m-30) cc_final: 0.6780 (m-30) REVERT: B 728 LYS cc_start: 0.8076 (pttm) cc_final: 0.7685 (pttm) REVERT: B 733 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: B 751 MET cc_start: 0.8180 (mmm) cc_final: 0.7606 (mmm) REVERT: B 775 GLU cc_start: 0.8749 (tp30) cc_final: 0.8215 (mm-30) REVERT: B 991 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6768 (mm-30) REVERT: B 995 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 1022 LYS cc_start: 0.8307 (tttp) cc_final: 0.7851 (tptp) REVERT: B 1027 LYS cc_start: 0.7056 (mmmt) cc_final: 0.6431 (mmtm) REVERT: B 1047 ASP cc_start: 0.6636 (t70) cc_final: 0.6337 (t70) REVERT: B 1070 LEU cc_start: 0.7649 (tt) cc_final: 0.6919 (tp) REVERT: B 1107 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7827 (tttp) REVERT: B 1108 HIS cc_start: 0.6612 (m170) cc_final: 0.6281 (m170) REVERT: B 1116 SER cc_start: 0.8482 (t) cc_final: 0.8258 (p) REVERT: B 1120 ASN cc_start: 0.7340 (p0) cc_final: 0.7071 (p0) REVERT: B 1133 LYS cc_start: 0.6793 (ptmt) cc_final: 0.6318 (ttpp) REVERT: B 1144 GLU cc_start: 0.7110 (tp30) cc_final: 0.6791 (tp30) REVERT: B 1147 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6704 (mm-30) REVERT: B 1255 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7083 (mm-30) REVERT: B 1280 ASN cc_start: 0.7687 (m-40) cc_final: 0.7180 (p0) REVERT: B 1305 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 1323 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7081 (ptt180) REVERT: B 1354 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7258 (tptp) REVERT: B 1370 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6722 (mm-30) REVERT: B 1416 VAL cc_start: 0.8126 (m) cc_final: 0.7759 (p) REVERT: B 1426 ILE cc_start: 0.8221 (mm) cc_final: 0.7974 (mp) REVERT: B 1427 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.6831 (t0) REVERT: B 1432 GLU cc_start: 0.7189 (tp30) cc_final: 0.6968 (tp30) REVERT: G 6 ILE cc_start: 0.8029 (mm) cc_final: 0.7523 (tt) REVERT: G 30 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: G 48 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7954 (mmmm) REVERT: G 55 LYS cc_start: 0.8064 (mptt) cc_final: 0.7732 (mttt) REVERT: G 123 MET cc_start: 0.8131 (tmm) cc_final: 0.7910 (ppp) REVERT: G 130 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7289 (ttmm) REVERT: H 9 ASP cc_start: 0.7530 (t0) cc_final: 0.7221 (t0) REVERT: H 18 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: H 25 GLN cc_start: 0.8053 (tt0) cc_final: 0.7548 (tt0) REVERT: H 56 MET cc_start: 0.7227 (mtp) cc_final: 0.6882 (mtp) REVERT: H 57 ASP cc_start: 0.6619 (t0) cc_final: 0.6215 (m-30) REVERT: H 59 LYS cc_start: 0.7677 (mttp) cc_final: 0.7141 (tppp) REVERT: H 62 THR cc_start: 0.7884 (m) cc_final: 0.7642 (t) REVERT: H 128 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7524 (mtmm) outliers start: 60 outliers final: 43 residues processed: 449 average time/residue: 0.4914 time to fit residues: 332.9455 Evaluate side-chains 460 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 410 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1301 ASN Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 chunk 60 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 194 optimal weight: 0.2980 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 98 GLN B 477 HIS ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.237 Angle : 0.540 8.772 43654 Z= 0.290 Chirality : 0.040 0.181 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.162 178.209 7090 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 2.33 % Allowed : 14.91 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.15), residues: 1192 sheet: -0.10 (0.27), residues: 342 loop : -0.92 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B1005 HIS 0.006 0.001 HIS A 287 PHE 0.022 0.001 PHE G 88 TYR 0.017 0.001 TYR A1239 ARG 0.005 0.000 ARG B1408 *********************** 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 475 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 412 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 HIS cc_start: 0.6885 (p90) cc_final: 0.6588 (p90) REVERT: A 113 GLU cc_start: 0.7728 (tt0) cc_final: 0.6981 (tp30) REVERT: A 134 ASN cc_start: 0.8092 (m110) cc_final: 0.7712 (m110) REVERT: A 135 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7631 (tp30) REVERT: A 171 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5094 (mt-10) REVERT: A 309 LYS cc_start: 0.7310 (pttp) cc_final: 0.6990 (ptpt) REVERT: A 317 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 328 ILE cc_start: 0.6753 (pt) cc_final: 0.6537 (mt) REVERT: A 333 LYS cc_start: 0.7615 (tptp) cc_final: 0.6953 (tptp) REVERT: A 366 LYS cc_start: 0.6708 (mmmt) cc_final: 0.5542 (mppt) REVERT: A 367 ASP cc_start: 0.7157 (p0) cc_final: 0.6956 (p0) REVERT: A 379 TYR cc_start: 0.6943 (t80) cc_final: 0.6482 (t80) REVERT: A 993 MET cc_start: 0.6886 (tpt) cc_final: 0.5839 (tpt) REVERT: A 995 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 1011 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8175 (ptpt) REVERT: A 1029 ILE cc_start: 0.8559 (pt) cc_final: 0.8357 (pt) REVERT: A 1037 ASP cc_start: 0.7224 (m-30) cc_final: 0.6827 (m-30) REVERT: A 1099 TRP cc_start: 0.6799 (p90) cc_final: 0.6360 (p90) REVERT: A 1172 TRP cc_start: 0.8324 (p90) cc_final: 0.7827 (p90) REVERT: A 1185 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7568 (mtp180) REVERT: A 1187 SER cc_start: 0.8352 (m) cc_final: 0.8030 (p) REVERT: A 1211 ASN cc_start: 0.7521 (m110) cc_final: 0.6942 (m110) REVERT: A 1250 LYS cc_start: 0.7696 (mttt) cc_final: 0.7266 (mtmt) REVERT: A 1302 GLU cc_start: 0.7725 (tt0) cc_final: 0.7179 (tt0) REVERT: A 1305 GLU cc_start: 0.7710 (tp30) cc_final: 0.7456 (tp30) REVERT: A 1309 GLN cc_start: 0.7680 (mm110) cc_final: 0.7454 (mm-40) REVERT: A 1317 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6604 (mm-30) REVERT: A 1325 LEU cc_start: 0.7800 (mm) cc_final: 0.7483 (mp) REVERT: A 1356 LYS cc_start: 0.7236 (mmtp) cc_final: 0.6848 (mtpp) REVERT: A 1388 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7777 (ttpp) REVERT: A 1436 GLN cc_start: 0.6201 (tp-100) cc_final: 0.5704 (tp-100) REVERT: B 31 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7423 (tt) REVERT: B 89 ASN cc_start: 0.7758 (p0) cc_final: 0.7502 (p0) REVERT: B 102 GLU cc_start: 0.7478 (mp0) cc_final: 0.7154 (mp0) REVERT: B 103 LYS cc_start: 0.7443 (tptm) cc_final: 0.7127 (tptm) REVERT: B 168 GLU cc_start: 0.7621 (tp30) cc_final: 0.6883 (tt0) REVERT: B 169 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7617 (ptpt) REVERT: B 201 PHE cc_start: 0.7707 (t80) cc_final: 0.7497 (t80) REVERT: B 290 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7861 (mmmt) REVERT: B 298 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: B 309 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8188 (mtpp) REVERT: B 326 ARG cc_start: 0.7646 (tpp80) cc_final: 0.7258 (ttm110) REVERT: B 374 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 429 GLN cc_start: 0.7604 (mm-40) cc_final: 0.6989 (mm-40) REVERT: B 476 LYS cc_start: 0.8779 (mttm) cc_final: 0.8306 (mttm) REVERT: B 499 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 541 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7014 (tt0) REVERT: B 545 LYS cc_start: 0.7036 (mptt) cc_final: 0.6788 (mmtt) REVERT: B 550 LYS cc_start: 0.7316 (mppt) cc_final: 0.6923 (mppt) REVERT: B 564 LYS cc_start: 0.8652 (mttt) cc_final: 0.8148 (mttt) REVERT: B 571 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6791 (mt-10) REVERT: B 587 MET cc_start: 0.5832 (mtt) cc_final: 0.5568 (mtt) REVERT: B 591 LYS cc_start: 0.8809 (tmmt) cc_final: 0.8514 (tmtt) REVERT: B 710 ASN cc_start: 0.7207 (m110) cc_final: 0.6720 (m110) REVERT: B 719 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: B 726 ASP cc_start: 0.7320 (m-30) cc_final: 0.6833 (m-30) REVERT: B 733 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: B 751 MET cc_start: 0.8188 (mmm) cc_final: 0.7611 (mmm) REVERT: B 775 GLU cc_start: 0.8732 (tp30) cc_final: 0.8140 (mm-30) REVERT: B 865 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6951 (p0) REVERT: B 991 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6761 (mm-30) REVERT: B 995 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7264 (tm-30) REVERT: B 1022 LYS cc_start: 0.8187 (tttp) cc_final: 0.7751 (tptp) REVERT: B 1027 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6413 (mmtm) REVERT: B 1047 ASP cc_start: 0.6780 (t70) cc_final: 0.6478 (t70) REVERT: B 1064 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7359 (t80) REVERT: B 1070 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6720 (tp) REVERT: B 1107 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7824 (tttp) REVERT: B 1108 HIS cc_start: 0.6582 (m170) cc_final: 0.6265 (m170) REVERT: B 1116 SER cc_start: 0.8498 (t) cc_final: 0.8243 (p) REVERT: B 1120 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6987 (p0) REVERT: B 1133 LYS cc_start: 0.6727 (ptmt) cc_final: 0.6270 (ttpp) REVERT: B 1144 GLU cc_start: 0.7105 (tp30) cc_final: 0.6785 (tp30) REVERT: B 1147 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6812 (mm-30) REVERT: B 1255 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 1280 ASN cc_start: 0.7667 (m-40) cc_final: 0.7170 (p0) REVERT: B 1305 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 1323 ARG cc_start: 0.7549 (ttp80) cc_final: 0.7060 (ptt180) REVERT: B 1354 LYS cc_start: 0.7467 (ttpt) cc_final: 0.7241 (tptp) REVERT: B 1370 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6745 (mm-30) REVERT: B 1416 VAL cc_start: 0.8122 (m) cc_final: 0.7777 (p) REVERT: B 1426 ILE cc_start: 0.8209 (mm) cc_final: 0.7969 (mp) REVERT: B 1427 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.6882 (t0) REVERT: B 1440 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6964 (mt-10) REVERT: G 6 ILE cc_start: 0.7999 (mm) cc_final: 0.7520 (tt) REVERT: G 12 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6971 (tt) REVERT: G 30 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: G 48 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7937 (mmmm) REVERT: G 55 LYS cc_start: 0.8083 (mptt) cc_final: 0.7748 (mttt) REVERT: H 9 ASP cc_start: 0.7499 (t0) cc_final: 0.7176 (t0) REVERT: H 18 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: H 25 GLN cc_start: 0.7994 (tt0) cc_final: 0.7486 (tt0) REVERT: H 57 ASP cc_start: 0.6479 (t0) cc_final: 0.6098 (m-30) REVERT: H 59 LYS cc_start: 0.7647 (mttp) cc_final: 0.7025 (tppp) REVERT: H 62 THR cc_start: 0.7865 (m) cc_final: 0.7629 (t) outliers start: 63 outliers final: 42 residues processed: 445 average time/residue: 0.4853 time to fit residues: 324.6876 Evaluate side-chains 460 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 405 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1064 TYR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1120 ASN Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1256 LEU Chi-restraints excluded: chain B residue 1301 ASN Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 270 optimal weight: 0.5980 chunk 284 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31440 Z= 0.210 Angle : 0.539 14.183 43654 Z= 0.286 Chirality : 0.039 0.175 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.132 177.901 7090 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 2.04 % Allowed : 15.47 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.15), residues: 2913 helix: 1.31 (0.15), residues: 1193 sheet: -0.07 (0.27), residues: 342 loop : -0.89 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1005 HIS 0.006 0.001 HIS A 287 PHE 0.020 0.001 PHE G 88 TYR 0.019 0.001 TYR A 186 ARG 0.004 0.000 ARG B1408 *********************** 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 464 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 409 time to evaluate : 2.910 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 79 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6541 (tm-30) REVERT: A 94 HIS cc_start: 0.6888 (p90) cc_final: 0.6589 (p90) REVERT: A 113 GLU cc_start: 0.7752 (tt0) cc_final: 0.6959 (tp30) REVERT: A 134 ASN cc_start: 0.8089 (m110) cc_final: 0.7710 (m110) REVERT: A 135 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7649 (tp30) REVERT: A 171 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5083 (mt-10) REVERT: A 181 HIS cc_start: 0.7089 (t-90) cc_final: 0.6635 (m-70) REVERT: A 187 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6609 (mm-40) REVERT: A 297 TYR cc_start: 0.4863 (t80) cc_final: 0.4634 (t80) REVERT: A 303 ASN cc_start: 0.6827 (t0) cc_final: 0.6009 (p0) REVERT: A 304 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 309 LYS cc_start: 0.7297 (pttp) cc_final: 0.6933 (ptpt) REVERT: A 317 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6891 (mm-30) REVERT: A 328 ILE cc_start: 0.6753 (pt) cc_final: 0.6519 (mt) REVERT: A 366 LYS cc_start: 0.6738 (mmmt) cc_final: 0.5587 (mppt) REVERT: A 379 TYR cc_start: 0.6905 (t80) cc_final: 0.6484 (t80) REVERT: A 684 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 993 MET cc_start: 0.6879 (tpt) cc_final: 0.5839 (tpt) REVERT: A 995 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 1011 LYS cc_start: 0.8579 (ptpt) cc_final: 0.8190 (ptpt) REVERT: A 1037 ASP cc_start: 0.7251 (m-30) cc_final: 0.6795 (m-30) REVERT: A 1099 TRP cc_start: 0.6770 (p90) cc_final: 0.6430 (p90) REVERT: A 1172 TRP cc_start: 0.8321 (p90) cc_final: 0.7885 (p90) REVERT: A 1187 SER cc_start: 0.8377 (m) cc_final: 0.8043 (p) REVERT: A 1211 ASN cc_start: 0.7529 (m110) cc_final: 0.6949 (m110) REVERT: A 1250 LYS cc_start: 0.7692 (mttt) cc_final: 0.7295 (mtmm) REVERT: A 1302 GLU cc_start: 0.7722 (tt0) cc_final: 0.7160 (tt0) REVERT: A 1305 GLU cc_start: 0.7706 (tp30) cc_final: 0.7450 (tp30) REVERT: A 1309 GLN cc_start: 0.7670 (mm110) cc_final: 0.7439 (mm-40) REVERT: A 1317 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6579 (mm-30) REVERT: A 1325 LEU cc_start: 0.7788 (mm) cc_final: 0.7474 (mp) REVERT: A 1388 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7857 (ttpp) REVERT: A 1436 GLN cc_start: 0.6182 (tp-100) cc_final: 0.5686 (tp-100) REVERT: B 89 ASN cc_start: 0.7766 (p0) cc_final: 0.7543 (p0) REVERT: B 103 LYS cc_start: 0.7462 (tptm) cc_final: 0.7142 (tptm) REVERT: B 168 GLU cc_start: 0.7612 (tp30) cc_final: 0.6893 (tt0) REVERT: B 290 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7850 (mmmt) REVERT: B 298 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: B 326 ARG cc_start: 0.7641 (tpp80) cc_final: 0.7246 (ttm110) REVERT: B 374 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7471 (mm-30) REVERT: B 429 GLN cc_start: 0.7589 (mm-40) cc_final: 0.6887 (mm-40) REVERT: B 476 LYS cc_start: 0.8727 (mttm) cc_final: 0.8228 (mttm) REVERT: B 499 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 541 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6999 (tt0) REVERT: B 545 LYS cc_start: 0.7037 (mptt) cc_final: 0.6777 (mmtt) REVERT: B 564 LYS cc_start: 0.8641 (mttt) cc_final: 0.8162 (mttt) REVERT: B 571 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6664 (mt-10) REVERT: B 587 MET cc_start: 0.5821 (mtt) cc_final: 0.5497 (mtt) REVERT: B 591 LYS cc_start: 0.8823 (tmmt) cc_final: 0.8526 (tmtt) REVERT: B 707 ASP cc_start: 0.7622 (t0) cc_final: 0.7420 (m-30) REVERT: B 710 ASN cc_start: 0.7198 (m110) cc_final: 0.6736 (m110) REVERT: B 719 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7326 (mp0) REVERT: B 726 ASP cc_start: 0.7328 (m-30) cc_final: 0.6816 (m-30) REVERT: B 728 LYS cc_start: 0.8091 (pttm) cc_final: 0.7674 (ptpt) REVERT: B 733 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 751 MET cc_start: 0.8176 (mmm) cc_final: 0.7604 (mmm) REVERT: B 775 GLU cc_start: 0.8739 (tp30) cc_final: 0.8155 (mm-30) REVERT: B 865 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6937 (p0) REVERT: B 991 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6761 (mm-30) REVERT: B 995 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 1022 LYS cc_start: 0.8213 (tttp) cc_final: 0.7776 (tptp) REVERT: B 1027 LYS cc_start: 0.6971 (mmmt) cc_final: 0.6634 (mmtt) REVERT: B 1047 ASP cc_start: 0.6831 (t70) cc_final: 0.6520 (t70) REVERT: B 1070 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6797 (tp) REVERT: B 1107 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7806 (tttp) REVERT: B 1108 HIS cc_start: 0.6572 (m170) cc_final: 0.6238 (m170) REVERT: B 1116 SER cc_start: 0.8498 (t) cc_final: 0.8248 (p) REVERT: B 1133 LYS cc_start: 0.6705 (ptmt) cc_final: 0.6252 (ttpp) REVERT: B 1144 GLU cc_start: 0.7094 (tp30) cc_final: 0.6790 (tp30) REVERT: B 1147 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6797 (mm-30) REVERT: B 1255 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7105 (mm-30) REVERT: B 1269 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7309 (mtmm) REVERT: B 1280 ASN cc_start: 0.7649 (m-40) cc_final: 0.7204 (p0) REVERT: B 1305 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7341 (mm-30) REVERT: B 1323 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7064 (ptt180) REVERT: B 1354 LYS cc_start: 0.7463 (ttpt) cc_final: 0.7232 (tptp) REVERT: B 1370 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6749 (mm-30) REVERT: B 1416 VAL cc_start: 0.8080 (m) cc_final: 0.7814 (p) REVERT: B 1426 ILE cc_start: 0.8199 (mm) cc_final: 0.7955 (mp) REVERT: B 1427 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6903 (t0) REVERT: B 1440 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7030 (mt-10) REVERT: G 9 ASP cc_start: 0.6640 (t70) cc_final: 0.6224 (t70) REVERT: G 12 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6976 (tt) REVERT: G 30 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6390 (pm20) REVERT: G 55 LYS cc_start: 0.8085 (mptt) cc_final: 0.7745 (mttt) REVERT: H 9 ASP cc_start: 0.7525 (t0) cc_final: 0.7172 (t0) REVERT: H 18 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: H 25 GLN cc_start: 0.7870 (tt0) cc_final: 0.7350 (tt0) REVERT: H 57 ASP cc_start: 0.6441 (t0) cc_final: 0.6070 (m-30) REVERT: H 59 LYS cc_start: 0.7598 (mttp) cc_final: 0.6980 (tppp) REVERT: H 62 THR cc_start: 0.7874 (m) cc_final: 0.7637 (t) outliers start: 55 outliers final: 40 residues processed: 436 average time/residue: 0.5403 time to fit residues: 359.3744 Evaluate side-chains 451 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 401 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE 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 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1301 ASN Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 18 ASP 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 187 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 291 optimal weight: 0.4980 chunk 252 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 551 HIS ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31440 Z= 0.258 Angle : 0.566 15.340 43654 Z= 0.299 Chirality : 0.040 0.166 4937 Planarity : 0.003 0.041 4540 Dihedral : 20.152 177.455 7090 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 2.04 % Allowed : 15.91 % Favored : 82.05 % 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: 0.10 (0.15), residues: 2913 helix: 1.24 (0.15), residues: 1192 sheet: -0.11 (0.27), residues: 342 loop : -0.92 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1005 HIS 0.006 0.001 HIS A 287 PHE 0.021 0.001 PHE B 201 TYR 0.024 0.001 TYR A 353 ARG 0.004 0.000 ARG A1185 ********************** 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 465 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 410 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6538 (tm-30) REVERT: A 94 HIS cc_start: 0.6886 (p90) cc_final: 0.6601 (p90) REVERT: A 113 GLU cc_start: 0.7726 (tt0) cc_final: 0.6911 (tp30) REVERT: A 134 ASN cc_start: 0.8125 (m110) cc_final: 0.7742 (m110) REVERT: A 135 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7674 (tp30) REVERT: A 156 TYR cc_start: 0.6597 (m-10) cc_final: 0.6377 (m-10) REVERT: A 171 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5090 (mt-10) REVERT: A 181 HIS cc_start: 0.7131 (t-90) cc_final: 0.6692 (m-70) REVERT: A 186 TYR cc_start: 0.7176 (t80) cc_final: 0.6607 (t80) REVERT: A 187 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6701 (mm-40) REVERT: A 301 LEU cc_start: 0.7906 (mp) cc_final: 0.7599 (mp) REVERT: A 309 LYS cc_start: 0.7252 (pttp) cc_final: 0.6877 (ptpt) REVERT: A 317 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6765 (mm-30) REVERT: A 321 TYR cc_start: 0.7227 (m-80) cc_final: 0.7026 (m-80) REVERT: A 328 ILE cc_start: 0.6750 (pt) cc_final: 0.6536 (mt) REVERT: A 366 LYS cc_start: 0.6681 (mmmt) cc_final: 0.5599 (mppt) REVERT: A 379 TYR cc_start: 0.6934 (t80) cc_final: 0.6500 (t80) REVERT: A 695 LYS cc_start: 0.7888 (tmmt) cc_final: 0.7520 (tmmt) REVERT: A 993 MET cc_start: 0.6891 (tpt) cc_final: 0.5859 (tpt) REVERT: A 995 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 1011 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8212 (ptpt) REVERT: A 1037 ASP cc_start: 0.7255 (m-30) cc_final: 0.6850 (m-30) REVERT: A 1099 TRP cc_start: 0.6813 (p90) cc_final: 0.6467 (p90) REVERT: A 1172 TRP cc_start: 0.8403 (p90) cc_final: 0.7961 (p90) REVERT: A 1187 SER cc_start: 0.8398 (m) cc_final: 0.8053 (p) REVERT: A 1211 ASN cc_start: 0.7532 (m110) cc_final: 0.6968 (m110) REVERT: A 1250 LYS cc_start: 0.7823 (mttt) cc_final: 0.7343 (mtmt) REVERT: A 1302 GLU cc_start: 0.7711 (tt0) cc_final: 0.7156 (tt0) REVERT: A 1305 GLU cc_start: 0.7708 (tp30) cc_final: 0.7488 (tp30) REVERT: A 1317 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6562 (mm-30) REVERT: A 1325 LEU cc_start: 0.7810 (mm) cc_final: 0.7497 (mp) REVERT: A 1388 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7857 (ttpp) REVERT: A 1436 GLN cc_start: 0.6189 (tp-100) cc_final: 0.5687 (tp-100) REVERT: B 89 ASN cc_start: 0.7755 (p0) cc_final: 0.7543 (p0) REVERT: B 90 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: B 103 LYS cc_start: 0.7508 (tptm) cc_final: 0.7175 (tptm) REVERT: B 168 GLU cc_start: 0.7632 (tp30) cc_final: 0.6901 (tt0) REVERT: B 201 PHE cc_start: 0.7798 (t80) cc_final: 0.7571 (t80) REVERT: B 290 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7860 (mmmt) REVERT: B 298 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: B 326 ARG cc_start: 0.7670 (tpp80) cc_final: 0.7286 (ttm110) REVERT: B 374 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 429 GLN cc_start: 0.7600 (mm-40) cc_final: 0.6875 (mm-40) REVERT: B 476 LYS cc_start: 0.8716 (mttm) cc_final: 0.8224 (mttm) REVERT: B 499 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6937 (mm-30) REVERT: B 541 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7104 (tt0) REVERT: B 564 LYS cc_start: 0.8647 (mttt) cc_final: 0.8172 (mttt) REVERT: B 571 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6606 (mt-10) REVERT: B 587 MET cc_start: 0.5978 (mtt) cc_final: 0.5634 (mtt) REVERT: B 591 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8521 (tmtt) REVERT: B 710 ASN cc_start: 0.7186 (m110) cc_final: 0.6728 (m110) REVERT: B 719 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 726 ASP cc_start: 0.7349 (m-30) cc_final: 0.6837 (m-30) REVERT: B 728 LYS cc_start: 0.8134 (pttm) cc_final: 0.7723 (ptpt) REVERT: B 733 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: B 751 MET cc_start: 0.8174 (mmm) cc_final: 0.7606 (mmm) REVERT: B 775 GLU cc_start: 0.8743 (tp30) cc_final: 0.8174 (mm-30) REVERT: B 865 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6954 (p0) REVERT: B 991 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 995 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7306 (tm-30) REVERT: B 1022 LYS cc_start: 0.8260 (tttp) cc_final: 0.7812 (tptp) REVERT: B 1027 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6589 (mmtt) REVERT: B 1047 ASP cc_start: 0.6958 (t70) cc_final: 0.6624 (t70) REVERT: B 1070 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6871 (tp) REVERT: B 1107 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7820 (tttp) REVERT: B 1108 HIS cc_start: 0.6602 (m170) cc_final: 0.6281 (m170) REVERT: B 1116 SER cc_start: 0.8499 (t) cc_final: 0.8260 (p) REVERT: B 1133 LYS cc_start: 0.6716 (ptmt) cc_final: 0.6312 (ttpp) REVERT: B 1144 GLU cc_start: 0.7057 (tp30) cc_final: 0.6755 (tp30) REVERT: B 1147 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6801 (mm-30) REVERT: B 1163 THR cc_start: 0.8602 (t) cc_final: 0.8260 (p) REVERT: B 1255 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 1269 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7329 (mtmm) REVERT: B 1280 ASN cc_start: 0.7656 (m-40) cc_final: 0.7235 (p0) REVERT: B 1305 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 1323 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7105 (ptt180) REVERT: B 1341 GLU cc_start: 0.6653 (tp30) cc_final: 0.6279 (tp30) REVERT: B 1354 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7274 (tptp) REVERT: B 1370 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6775 (mm-30) REVERT: B 1416 VAL cc_start: 0.8106 (m) cc_final: 0.7819 (p) REVERT: B 1426 ILE cc_start: 0.8209 (mm) cc_final: 0.7970 (mp) REVERT: B 1427 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6915 (t0) REVERT: B 1440 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6953 (mt-10) REVERT: G 12 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.7086 (tt) REVERT: G 30 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: G 55 LYS cc_start: 0.8091 (mptt) cc_final: 0.7746 (mttt) REVERT: G 87 GLN cc_start: 0.7909 (tt0) cc_final: 0.7434 (tt0) REVERT: H 9 ASP cc_start: 0.7539 (t0) cc_final: 0.7212 (t0) REVERT: H 25 GLN cc_start: 0.8000 (tt0) cc_final: 0.7511 (tt0) REVERT: H 57 ASP cc_start: 0.6514 (t0) cc_final: 0.6125 (m-30) REVERT: H 59 LYS cc_start: 0.7610 (mttp) cc_final: 0.6985 (tppp) REVERT: H 62 THR cc_start: 0.7876 (m) cc_final: 0.7615 (t) outliers start: 55 outliers final: 41 residues processed: 441 average time/residue: 0.4931 time to fit residues: 330.5328 Evaluate side-chains 455 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1248 ILE Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1301 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 733 GLN Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 761 ARG Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 965 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain B residue 1173 VAL Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1236 ILE Chi-restraints excluded: chain B residue 1238 LYS Chi-restraints excluded: chain B residue 1301 ASN Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1427 ASN Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain H residue 60 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 31 optimal weight: 0.0000 chunk 46 optimal weight: 50.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN B 410 GLN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.217701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164768 restraints weight = 46340.236| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.68 r_work: 0.3672 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31440 Z= 0.251 Angle : 0.560 15.477 43654 Z= 0.297 Chirality : 0.040 0.157 4937 Planarity : 0.003 0.057 4540 Dihedral : 20.155 178.103 7090 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.04 % Allowed : 16.10 % Favored : 81.87 % 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: 0.10 (0.15), residues: 2913 helix: 1.24 (0.15), residues: 1198 sheet: -0.10 (0.27), residues: 349 loop : -0.94 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1005 HIS 0.006 0.001 HIS A 287 PHE 0.020 0.001 PHE G 88 TYR 0.019 0.001 TYR A 353 ARG 0.005 0.000 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.01 seconds wall clock time: 141 minutes 6.09 seconds (8466.09 seconds total)