Starting phenix.real_space_refine on Fri Aug 7 22:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k18_61968/08_2026/9k18_61968.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 7 6.06 5 P 34 5.49 5 S 141 5.16 5 C 14822 2.51 5 N 4125 2.21 5 O 4562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23692 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6672 Classifications: {'peptide': 854} Link IDs: {'PTRANS': 27, 'TRANS': 826} Chain: "B" Number of atoms: 7995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7995 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 37, 'TRANS': 968} Chain breaks: 2 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2340 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1698 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "H" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1135 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "I" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 713 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 514 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "K" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 887 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 375 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "N" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15372 SG CYS C 91 82.874 43.956 137.240 1.00101.77 S ATOM 15391 SG CYS C 94 83.724 40.360 134.489 1.00124.44 S ATOM 20732 SG CYS I 29 32.321 48.281 20.147 1.00 70.70 S ATOM 21292 SG CYS J 10 52.912 44.323 121.375 1.00 52.02 S ATOM 21558 SG CYS J 44 50.367 45.564 119.354 1.00 50.71 S Time building chain proxies: 4.99, per 1000 atoms: 0.21 Number of scatterers: 23692 At special positions: 0 Unit cell: (118.26, 141.255, 164.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Ca 1 19.99 S 141 16.00 P 34 15.00 O 4562 8.00 N 4125 7.00 C 14822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2101 " pdb="ZN ZN A2101 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A2101 " - pdb=" NE2 HIS A 940 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 32 sheets defined 33.8% alpha, 14.5% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.715A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 541 through 547 removed outlier: 3.725A pdb=" N LEU A 547 " --> pdb=" O GLN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.561A pdb=" N ILE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 removed outlier: 3.737A pdb=" N ALA A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.829A pdb=" N GLU A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 648 Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 656 through 674 removed outlier: 4.340A pdb=" N GLU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.627A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.733A pdb=" N LYS A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.813A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 744 through 748 Processing helix chain 'A' and resid 750 through 771 Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.529A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.507A pdb=" N MET A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 904 removed outlier: 3.606A pdb=" N THR A 898 " --> pdb=" O ASN A 894 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 899 " --> pdb=" O SER A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 968 removed outlier: 4.014A pdb=" N LEU A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 removed outlier: 3.785A pdb=" N ALA A1012 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1013 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 4.464A pdb=" N VAL A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1096 through 1099 removed outlier: 3.651A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1099' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1137 removed outlier: 4.175A pdb=" N GLU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 3.706A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1173 removed outlier: 3.813A pdb=" N LEU A1172 " --> pdb=" O GLY A1168 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A1173 " --> pdb=" O TYR A1169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1168 through 1173' Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.707A pdb=" N SER B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.531A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.859A pdb=" N THR B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU B 183 " --> pdb=" O ASN B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.973A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.657A pdb=" N TYR B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 removed outlier: 4.058A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 337' Processing helix chain 'B' and resid 360 through 380 removed outlier: 3.934A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 420 Processing helix chain 'B' and resid 421 through 426 removed outlier: 4.010A pdb=" N LEU B 426 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 546 through 552 removed outlier: 3.872A pdb=" N GLY B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.585A pdb=" N LYS B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.759A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.909A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.607A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.861A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.575A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 967 removed outlier: 4.504A pdb=" N LEU B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1005 Processing helix chain 'B' and resid 1040 through 1045 removed outlier: 3.652A pdb=" N ASP B1043 " --> pdb=" O MET B1040 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B1045 " --> pdb=" O GLU B1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.656A pdb=" N ALA C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.601A pdb=" N LEU C 74 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.601A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.649A pdb=" N VAL C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 297 No H-bonds generated for 'chain 'C' and resid 296 through 297' Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.057A pdb=" N THR C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.801A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.947A pdb=" N ILE E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 60' Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.665A pdb=" N PHE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.516A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.858A pdb=" N LEU E 156 " --> pdb=" O THR E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.695A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.828A pdb=" N GLN E 189 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 190' Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.736A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.889A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.553A pdb=" N TYR J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 50 removed outlier: 3.594A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.617A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 330 removed outlier: 4.126A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 455 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 7.094A pdb=" N VAL H 92 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG H 144 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR H 59 " --> pdb=" O ARG H 144 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 114 " --> pdb=" O MET H 121 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU H 111 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE H 100 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AA6, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.306A pdb=" N ASN A 799 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 805 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 876 through 879 Processing sheet with id=AA9, first strand: chain 'A' and resid 1003 through 1004 removed outlier: 6.644A pdb=" N HIS A 938 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE A 915 " --> pdb=" O HIS A 938 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 940 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 917 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 97 removed outlier: 5.634A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 125 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AB3, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.531A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AB7, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.529A pdb=" N ILE B 658 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 627 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AB9, first strand: chain 'B' and resid 575 through 580 removed outlier: 7.074A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 738 through 741 removed outlier: 3.516A pdb=" N ASN B 892 " --> pdb=" O VAL B 808 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 896 " --> pdb=" O TYR B 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 738 through 741 removed outlier: 6.443A pdb=" N TYR B 893 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 884 " --> pdb=" O TYR B 893 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 895 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 882 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER B 897 " --> pdb=" O GLN B 880 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 7.079A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 855 through 857 removed outlier: 6.944A pdb=" N VAL B 869 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.821A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.821A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 191 " --> pdb=" O LYS C 262 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.247A pdb=" N GLU C 162 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS C 164 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE C 56 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG C 166 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 54 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 168 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AC9, first strand: chain 'C' and resid 221 through 224 removed outlier: 3.523A pdb=" N ASP C 224 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 229 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 96 through 97 removed outlier: 7.940A pdb=" N VAL E 96 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 127 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 192 through 194 Processing sheet with id=AD3, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.599A pdb=" N ARG F 116 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 14 through 19 removed outlier: 4.086A pdb=" N ILE I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.564A pdb=" N ILE K 75 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7349 1.33 - 1.45: 3704 1.45 - 1.57: 12846 1.57 - 1.70: 66 1.70 - 1.82: 218 Bond restraints: 24183 Sorted by residual: bond pdb=" C1' DC N 13 " pdb=" N1 DC N 13 " ideal model delta sigma weight residual 1.468 1.555 -0.087 1.40e-02 5.10e+03 3.87e+01 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" C1' DG N 17 " pdb=" N9 DG N 17 " ideal model delta sigma weight residual 1.468 1.394 0.074 1.40e-02 5.10e+03 2.76e+01 bond pdb=" C1' DG N 12 " pdb=" N9 DG N 12 " ideal model delta sigma weight residual 1.468 1.411 0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" C3' DG N 31 " pdb=" C2' DG N 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.66e+00 ... (remaining 24178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 32182 2.15 - 4.30: 503 4.30 - 6.45: 68 6.45 - 8.61: 8 8.61 - 10.76: 2 Bond angle restraints: 32763 Sorted by residual: angle pdb=" O4' DA N 22 " pdb=" C4' DA N 22 " pdb=" C3' DA N 22 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.22e+01 angle pdb=" O4' DA T 7 " pdb=" C4' DA T 7 " pdb=" C3' DA T 7 " ideal model delta sigma weight residual 106.00 102.91 3.09 6.00e-01 2.78e+00 2.65e+01 angle pdb=" N GLU B 332 " pdb=" CA GLU B 332 " pdb=" C GLU B 332 " ideal model delta sigma weight residual 114.75 108.30 6.45 1.26e+00 6.30e-01 2.62e+01 angle pdb=" O4' DT T 10 " pdb=" C4' DT T 10 " pdb=" C3' DT T 10 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.26e+01 angle pdb=" C TYR C 190 " pdb=" N GLU C 191 " pdb=" CA GLU C 191 " ideal model delta sigma weight residual 121.61 115.09 6.52 1.39e+00 5.18e-01 2.20e+01 ... (remaining 32758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13062 17.94 - 35.88: 1177 35.88 - 53.83: 332 53.83 - 71.77: 61 71.77 - 89.71: 23 Dihedral angle restraints: 14655 sinusoidal: 6225 harmonic: 8430 Sorted by residual: dihedral pdb=" CA SER B 561 " pdb=" C SER B 561 " pdb=" N THR B 562 " pdb=" CA THR B 562 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ARG A 522 " pdb=" C ARG A 522 " pdb=" N SER A 523 " pdb=" CA SER A 523 " ideal model delta harmonic sigma weight residual 180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LEU H 135 " pdb=" C LEU H 135 " pdb=" N ASP H 136 " pdb=" CA ASP H 136 " ideal model delta harmonic sigma weight residual 180.00 154.92 25.08 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 14652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2425 0.039 - 0.078: 918 0.078 - 0.117: 276 0.117 - 0.156: 47 0.156 - 0.195: 6 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA ASN B 729 " pdb=" N ASN B 729 " pdb=" C ASN B 729 " pdb=" CB ASN B 729 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CG LEU L 21 " pdb=" CB LEU L 21 " pdb=" CD1 LEU L 21 " pdb=" CD2 LEU L 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB THR B 362 " pdb=" CA THR B 362 " pdb=" OG1 THR B 362 " pdb=" CG2 THR B 362 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 3669 not shown) Planarity restraints: 4113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 135 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ASP F 135 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP F 135 " -0.024 2.00e-02 2.50e+03 pdb=" N SER F 136 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 144 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ARG H 144 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG H 144 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS H 145 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 729 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ASN B 729 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN B 729 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 730 " -0.014 2.00e-02 2.50e+03 ... (remaining 4110 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 14 2.45 - 3.06: 15222 3.06 - 3.67: 33699 3.67 - 4.29: 48926 4.29 - 4.90: 81789 Nonbonded interactions: 179650 Sorted by model distance: nonbonded pdb=" OE1 GLU A1018 " pdb=" NH2 ARG I 20 " model vdw 1.833 3.120 nonbonded pdb=" CG GLU A1018 " pdb=" NH2 ARG I 20 " model vdw 2.140 3.520 nonbonded pdb=" C VAL H 92 " pdb="ZN ZN H 201 " model vdw 2.176 2.460 nonbonded pdb=" N MET H 93 " pdb="ZN ZN H 201 " model vdw 2.184 2.310 nonbonded pdb=" CB GLU A1018 " pdb=" NH2 ARG I 20 " model vdw 2.194 3.520 ... (remaining 179645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.087 24190 Z= 0.226 Angle : 0.681 10.758 32763 Z= 0.419 Chirality : 0.044 0.195 3672 Planarity : 0.004 0.048 4113 Dihedral : 15.260 89.709 9201 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.20 % Favored : 89.77 % Rotamer: Outliers : 1.80 % Allowed : 10.82 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 2873 helix: 0.04 (0.19), residues: 803 sheet: -1.34 (0.28), residues: 392 loop : -2.19 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 450 TYR 0.030 0.002 TYR B 267 PHE 0.024 0.001 PHE B 321 TRP 0.016 0.001 TRP B 576 HIS 0.009 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.23 (24183) covalent geometry : angle 0.68069 / 0.42 (32763) hydrogen bonds : bond 0.19908 / 13.65 ( 753) hydrogen bonds : angle 6.87631 / 4.72 ( 2075) metal coordination : bond 0.00468 / 0.23 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6979 (mmpt) cc_final: 0.5767 (tptp) REVERT: A 371 MET cc_start: 0.4662 (mmm) cc_final: 0.4336 (mmm) REVERT: A 420 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.4836 (mmtm) REVERT: A 981 MET cc_start: 0.7474 (ptt) cc_final: 0.7180 (ppp) REVERT: A 1006 MET cc_start: 0.7207 (mtm) cc_final: 0.6838 (mtm) REVERT: A 1028 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8103 (pp) REVERT: B 495 TYR cc_start: 0.3122 (OUTLIER) cc_final: 0.2229 (t80) REVERT: C 204 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7354 (pp) REVERT: E 189 GLN cc_start: 0.7778 (mt0) cc_final: 0.7204 (mm110) REVERT: F 92 GLU cc_start: 0.7917 (mp0) cc_final: 0.7642 (mp0) REVERT: H 46 ASN cc_start: 0.7520 (t0) cc_final: 0.7177 (t0) REVERT: I 30 ARG cc_start: 0.7030 (tpp-160) cc_final: 0.6815 (tpm170) REVERT: J 54 ASP cc_start: 0.7466 (t0) cc_final: 0.7248 (t0) outliers start: 46 outliers final: 38 residues processed: 278 average time/residue: 0.1689 time to fit residues: 73.1170 Evaluate side-chains 242 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 222 SER Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 GLN I 31 ASN I 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080548 restraints weight = 54233.954| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.19 r_work: 0.2996 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24190 Z= 0.200 Angle : 0.641 8.937 32763 Z= 0.346 Chirality : 0.046 0.294 3672 Planarity : 0.004 0.051 4113 Dihedral : 13.019 88.892 3609 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.89 % Favored : 89.07 % Rotamer: Outliers : 2.73 % Allowed : 11.95 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 2873 helix: 0.06 (0.18), residues: 836 sheet: -1.23 (0.27), residues: 408 loop : -2.25 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 920 TYR 0.019 0.002 TYR B 267 PHE 0.026 0.002 PHE B 321 TRP 0.013 0.001 TRP B 510 HIS 0.006 0.001 HIS K 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (24183) covalent geometry : angle 0.64089 / 0.35 (32763) hydrogen bonds : bond 0.05329 / 3.60 ( 753) hydrogen bonds : angle 5.40315 / 3.75 ( 2075) metal coordination : bond 0.00522 / 0.26 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.7002 (mmpt) cc_final: 0.5665 (tptp) REVERT: A 371 MET cc_start: 0.4917 (mmm) cc_final: 0.4464 (mmm) REVERT: A 420 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.4687 (mmtm) REVERT: A 981 MET cc_start: 0.7861 (ptt) cc_final: 0.7530 (ppp) REVERT: A 1006 MET cc_start: 0.8001 (mtm) cc_final: 0.7496 (mtm) REVERT: A 1028 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8065 (pp) REVERT: A 1048 ILE cc_start: 0.9294 (mt) cc_final: 0.9063 (mt) REVERT: B 68 MET cc_start: 0.7321 (tpt) cc_final: 0.6659 (ptp) REVERT: B 392 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8810 (ptt90) REVERT: B 495 TYR cc_start: 0.3539 (OUTLIER) cc_final: 0.2906 (t80) REVERT: E 189 GLN cc_start: 0.7937 (mt0) cc_final: 0.7036 (mm110) REVERT: F 102 MET cc_start: 0.8170 (tmm) cc_final: 0.7949 (tmm) REVERT: H 46 ASN cc_start: 0.7596 (t0) cc_final: 0.7388 (t0) REVERT: I 30 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.6891 (tpm170) outliers start: 70 outliers final: 39 residues processed: 279 average time/residue: 0.1421 time to fit residues: 62.9025 Evaluate side-chains 239 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 85 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 178 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 GLN B 945 HIS L 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078983 restraints weight = 53931.942| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.10 r_work: 0.2986 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24190 Z= 0.175 Angle : 0.616 9.659 32763 Z= 0.330 Chirality : 0.045 0.278 3672 Planarity : 0.004 0.051 4113 Dihedral : 12.934 89.690 3586 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.55 % Favored : 89.42 % Rotamer: Outliers : 2.50 % Allowed : 13.94 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2873 helix: 0.21 (0.18), residues: 836 sheet: -1.17 (0.27), residues: 400 loop : -2.22 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.015 0.002 TYR B 267 PHE 0.024 0.001 PHE B 321 TRP 0.011 0.001 TRP B 510 HIS 0.006 0.001 HIS K 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (24183) covalent geometry : angle 0.61618 / 0.33 (32763) hydrogen bonds : bond 0.04930 / 3.31 ( 753) hydrogen bonds : angle 5.10822 / 3.54 ( 2075) metal coordination : bond 0.00425 / 0.21 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6930 (mmpt) cc_final: 0.5672 (tptp) REVERT: A 371 MET cc_start: 0.5069 (mmm) cc_final: 0.4658 (mmm) REVERT: A 395 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7588 (tptt) REVERT: A 417 THR cc_start: 0.4294 (OUTLIER) cc_final: 0.3955 (t) REVERT: A 420 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.4585 (mmtm) REVERT: A 858 MET cc_start: 0.8662 (mtp) cc_final: 0.8398 (mtp) REVERT: A 981 MET cc_start: 0.7903 (ptt) cc_final: 0.7490 (ppp) REVERT: A 1006 MET cc_start: 0.7985 (mtm) cc_final: 0.7485 (mtm) REVERT: A 1028 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 1048 ILE cc_start: 0.9279 (mt) cc_final: 0.9025 (mt) REVERT: B 68 MET cc_start: 0.7300 (tpt) cc_final: 0.6647 (ptp) REVERT: B 392 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8867 (ptt90) REVERT: B 495 TYR cc_start: 0.3389 (OUTLIER) cc_final: 0.2743 (t80) REVERT: C 204 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7527 (pp) REVERT: E 189 GLN cc_start: 0.7859 (mt0) cc_final: 0.6838 (mm110) REVERT: F 102 MET cc_start: 0.8230 (tmm) cc_final: 0.7987 (tmm) REVERT: H 46 ASN cc_start: 0.7601 (t0) cc_final: 0.7378 (t0) REVERT: I 30 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.6869 (tpm170) REVERT: K 97 GLU cc_start: 0.8589 (tp30) cc_final: 0.8012 (tp30) REVERT: K 108 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8664 (mm-30) outliers start: 64 outliers final: 42 residues processed: 265 average time/residue: 0.1698 time to fit residues: 71.1466 Evaluate side-chains 244 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 179 optimal weight: 0.0170 chunk 194 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 288 optimal weight: 40.0000 chunk 128 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078708 restraints weight = 53722.270| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.27 r_work: 0.2965 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24190 Z= 0.180 Angle : 0.606 8.093 32763 Z= 0.325 Chirality : 0.045 0.258 3672 Planarity : 0.004 0.051 4113 Dihedral : 12.905 87.969 3582 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.72 % Favored : 89.24 % Rotamer: Outliers : 3.16 % Allowed : 14.45 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.16), residues: 2873 helix: 0.30 (0.18), residues: 836 sheet: -1.18 (0.26), residues: 417 loop : -2.21 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.016 0.002 TYR B 804 PHE 0.023 0.001 PHE B 321 TRP 0.012 0.001 TRP B 510 HIS 0.006 0.001 HIS K 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (24183) covalent geometry : angle 0.60594 / 0.33 (32763) hydrogen bonds : bond 0.04627 / 3.08 ( 753) hydrogen bonds : angle 4.93147 / 3.42 ( 2075) metal coordination : bond 0.00434 / 0.22 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 212 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6932 (mmpt) cc_final: 0.5676 (tptp) REVERT: A 371 MET cc_start: 0.5040 (mmm) cc_final: 0.4597 (mmm) REVERT: A 417 THR cc_start: 0.4176 (OUTLIER) cc_final: 0.3794 (t) REVERT: A 420 LYS cc_start: 0.5589 (OUTLIER) cc_final: 0.4674 (mmtm) REVERT: A 858 MET cc_start: 0.8689 (mtp) cc_final: 0.8423 (mtp) REVERT: A 981 MET cc_start: 0.7931 (ptt) cc_final: 0.7500 (ppp) REVERT: A 1006 MET cc_start: 0.7992 (mtm) cc_final: 0.7496 (mtm) REVERT: A 1028 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8121 (pp) REVERT: A 1048 ILE cc_start: 0.9280 (mt) cc_final: 0.9000 (mt) REVERT: B 68 MET cc_start: 0.7308 (tpt) cc_final: 0.6660 (ptp) REVERT: B 392 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8874 (ptt90) REVERT: B 495 TYR cc_start: 0.3342 (OUTLIER) cc_final: 0.2624 (t80) REVERT: C 204 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7647 (pp) REVERT: E 129 GLN cc_start: 0.7972 (pm20) cc_final: 0.7717 (pm20) REVERT: E 189 GLN cc_start: 0.7867 (mt0) cc_final: 0.6945 (mm110) REVERT: F 92 GLU cc_start: 0.7948 (mp0) cc_final: 0.7652 (mp0) REVERT: F 102 MET cc_start: 0.8262 (tmm) cc_final: 0.8021 (tmm) REVERT: F 103 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8278 (mtpp) REVERT: H 30 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8196 (tp) REVERT: H 41 MET cc_start: 0.8023 (tpp) cc_final: 0.7377 (mpp) REVERT: H 46 ASN cc_start: 0.7637 (t0) cc_final: 0.7393 (t0) REVERT: I 30 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.6833 (tpm170) REVERT: K 108 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8636 (mm-30) outliers start: 81 outliers final: 49 residues processed: 279 average time/residue: 0.1670 time to fit residues: 73.4651 Evaluate side-chains 255 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 266 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077816 restraints weight = 53526.943| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.08 r_work: 0.2970 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24190 Z= 0.189 Angle : 0.614 7.784 32763 Z= 0.327 Chirality : 0.045 0.246 3672 Planarity : 0.004 0.053 4113 Dihedral : 12.884 87.902 3580 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.55 % Favored : 89.42 % Rotamer: Outliers : 3.24 % Allowed : 15.23 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2873 helix: 0.34 (0.18), residues: 835 sheet: -1.13 (0.26), residues: 420 loop : -2.20 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.017 0.001 TYR B 804 PHE 0.023 0.001 PHE B 321 TRP 0.013 0.001 TRP B 510 HIS 0.010 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (24183) covalent geometry : angle 0.61437 / 0.33 (32763) hydrogen bonds : bond 0.04637 / 3.08 ( 753) hydrogen bonds : angle 4.88427 / 3.39 ( 2075) metal coordination : bond 0.00445 / 0.22 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 208 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6905 (mmpt) cc_final: 0.5639 (tptp) REVERT: A 371 MET cc_start: 0.4991 (mmm) cc_final: 0.4585 (mmm) REVERT: A 417 THR cc_start: 0.4314 (OUTLIER) cc_final: 0.3935 (t) REVERT: A 420 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.4710 (mmtm) REVERT: A 788 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 858 MET cc_start: 0.8669 (mtp) cc_final: 0.8402 (mtp) REVERT: A 981 MET cc_start: 0.7922 (ptt) cc_final: 0.7477 (ppp) REVERT: A 1006 MET cc_start: 0.8018 (mtm) cc_final: 0.7512 (mtm) REVERT: A 1028 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8043 (pp) REVERT: A 1048 ILE cc_start: 0.9261 (mt) cc_final: 0.8971 (mt) REVERT: B 68 MET cc_start: 0.7347 (tpt) cc_final: 0.6664 (ptp) REVERT: B 392 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8850 (ptt90) REVERT: B 495 TYR cc_start: 0.3307 (OUTLIER) cc_final: 0.2633 (t80) REVERT: C 204 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7644 (pp) REVERT: E 189 GLN cc_start: 0.7831 (mt0) cc_final: 0.6918 (mm110) REVERT: F 92 GLU cc_start: 0.8011 (mp0) cc_final: 0.7582 (mp0) REVERT: F 102 MET cc_start: 0.8257 (tmm) cc_final: 0.7985 (tmm) REVERT: F 103 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8232 (mtpp) REVERT: H 30 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8118 (tp) REVERT: H 41 MET cc_start: 0.8024 (tpp) cc_final: 0.7218 (mpp) REVERT: H 46 ASN cc_start: 0.7646 (t0) cc_final: 0.7384 (t0) REVERT: H 141 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8328 (tm) REVERT: I 30 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.6782 (tpm170) REVERT: K 108 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8647 (mm-30) outliers start: 83 outliers final: 56 residues processed: 277 average time/residue: 0.1441 time to fit residues: 63.6733 Evaluate side-chains 261 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 972 LYS Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 ASN B 638 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 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 = 0.3817 r_free = 0.3817 target = 0.112414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078111 restraints weight = 53740.038| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.90 r_work: 0.2998 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24190 Z= 0.147 Angle : 0.584 9.013 32763 Z= 0.313 Chirality : 0.044 0.248 3672 Planarity : 0.004 0.047 4113 Dihedral : 12.809 89.180 3580 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.30 % Favored : 89.66 % Rotamer: Outliers : 2.89 % Allowed : 16.20 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2873 helix: 0.48 (0.19), residues: 831 sheet: -1.05 (0.26), residues: 425 loop : -2.15 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 52 TYR 0.014 0.001 TYR B 804 PHE 0.020 0.001 PHE B 321 TRP 0.010 0.001 TRP A 539 HIS 0.010 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24183) covalent geometry : angle 0.58432 / 0.31 (32763) hydrogen bonds : bond 0.04216 / 2.79 ( 753) hydrogen bonds : angle 4.76063 / 3.31 ( 2075) metal coordination : bond 0.00370 / 0.19 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6885 (mmpt) cc_final: 0.5620 (tptp) REVERT: A 371 MET cc_start: 0.4974 (mmm) cc_final: 0.4582 (mmm) REVERT: A 417 THR cc_start: 0.4326 (OUTLIER) cc_final: 0.3932 (t) REVERT: A 420 LYS cc_start: 0.5685 (OUTLIER) cc_final: 0.4629 (mmtm) REVERT: A 788 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 858 MET cc_start: 0.8662 (mtp) cc_final: 0.8403 (mtp) REVERT: A 981 MET cc_start: 0.7866 (ptt) cc_final: 0.7461 (ppp) REVERT: A 1006 MET cc_start: 0.7961 (mtm) cc_final: 0.7465 (mtm) REVERT: A 1028 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8078 (pp) REVERT: A 1048 ILE cc_start: 0.9246 (mt) cc_final: 0.8951 (mt) REVERT: B 68 MET cc_start: 0.7295 (tpt) cc_final: 0.6640 (ptp) REVERT: B 339 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8038 (pttm) REVERT: B 392 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8825 (ptt90) REVERT: B 495 TYR cc_start: 0.3312 (OUTLIER) cc_final: 0.2852 (t80) REVERT: C 204 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7703 (pp) REVERT: E 189 GLN cc_start: 0.7789 (mt0) cc_final: 0.6934 (mm110) REVERT: E 197 ASP cc_start: 0.7811 (t70) cc_final: 0.7497 (t0) REVERT: F 92 GLU cc_start: 0.8039 (mp0) cc_final: 0.7604 (mp0) REVERT: F 102 MET cc_start: 0.8256 (tmm) cc_final: 0.7978 (tmm) REVERT: F 103 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8231 (mtpp) REVERT: H 30 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8133 (tp) REVERT: H 40 PHE cc_start: 0.7543 (t80) cc_final: 0.7024 (t80) REVERT: H 41 MET cc_start: 0.8042 (tpp) cc_final: 0.7042 (mpp) REVERT: H 46 ASN cc_start: 0.7582 (t0) cc_final: 0.7305 (t0) REVERT: H 141 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8311 (tm) REVERT: I 30 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.6754 (tpm170) REVERT: K 108 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8692 (mm-30) outliers start: 74 outliers final: 56 residues processed: 267 average time/residue: 0.1522 time to fit residues: 65.2541 Evaluate side-chains 261 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 265 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 270 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 286 optimal weight: 50.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 638 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.112321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078961 restraints weight = 53232.747| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.16 r_work: 0.2991 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24190 Z= 0.148 Angle : 0.587 9.097 32763 Z= 0.311 Chirality : 0.044 0.253 3672 Planarity : 0.004 0.044 4113 Dihedral : 12.669 89.233 3573 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.27 % Favored : 89.70 % Rotamer: Outliers : 3.12 % Allowed : 16.20 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2873 helix: 0.49 (0.19), residues: 842 sheet: -1.02 (0.26), residues: 425 loop : -2.12 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 52 TYR 0.015 0.001 TYR B 804 PHE 0.019 0.001 PHE B 321 TRP 0.010 0.001 TRP B 510 HIS 0.008 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (24183) covalent geometry : angle 0.58659 / 0.31 (32763) hydrogen bonds : bond 0.04130 / 2.73 ( 753) hydrogen bonds : angle 4.70404 / 3.27 ( 2075) metal coordination : bond 0.00353 / 0.18 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 203 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6872 (mmpt) cc_final: 0.5597 (tptp) REVERT: A 371 MET cc_start: 0.4966 (mmm) cc_final: 0.4557 (mmm) REVERT: A 417 THR cc_start: 0.4438 (OUTLIER) cc_final: 0.4035 (t) REVERT: A 420 LYS cc_start: 0.5648 (OUTLIER) cc_final: 0.4636 (mmtm) REVERT: A 788 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 858 MET cc_start: 0.8662 (mtp) cc_final: 0.8415 (mtp) REVERT: A 981 MET cc_start: 0.7909 (ptt) cc_final: 0.7475 (ppp) REVERT: A 1006 MET cc_start: 0.7990 (mtm) cc_final: 0.7472 (mtm) REVERT: A 1028 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 1048 ILE cc_start: 0.9236 (mt) cc_final: 0.8937 (mt) REVERT: B 68 MET cc_start: 0.7308 (tpt) cc_final: 0.6597 (ptp) REVERT: B 339 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8069 (pttm) REVERT: B 392 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8843 (ptt90) REVERT: B 495 TYR cc_start: 0.3285 (OUTLIER) cc_final: 0.2853 (t80) REVERT: C 204 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7655 (pp) REVERT: E 86 ARG cc_start: 0.5057 (tmt170) cc_final: 0.4588 (tmm160) REVERT: E 189 GLN cc_start: 0.7786 (mt0) cc_final: 0.6923 (mm110) REVERT: E 197 ASP cc_start: 0.7836 (t70) cc_final: 0.7531 (t0) REVERT: F 92 GLU cc_start: 0.8046 (mp0) cc_final: 0.7676 (mp0) REVERT: F 102 MET cc_start: 0.8160 (tmm) cc_final: 0.7859 (tmm) REVERT: H 30 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8123 (tp) REVERT: H 40 PHE cc_start: 0.7601 (t80) cc_final: 0.7054 (t80) REVERT: H 41 MET cc_start: 0.8100 (tpp) cc_final: 0.7103 (mpp) REVERT: H 46 ASN cc_start: 0.7564 (t0) cc_final: 0.7289 (t0) REVERT: H 141 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8282 (tm) REVERT: K 108 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8722 (mm-30) REVERT: L 43 ARG cc_start: 0.8548 (tpt-90) cc_final: 0.8330 (tpt170) outliers start: 80 outliers final: 59 residues processed: 266 average time/residue: 0.1526 time to fit residues: 65.1339 Evaluate side-chains 264 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 63 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 123 optimal weight: 0.0570 chunk 252 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 247 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN B 638 GLN I 41 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079564 restraints weight = 53330.991| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.06 r_work: 0.3002 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24190 Z= 0.134 Angle : 0.571 8.890 32763 Z= 0.305 Chirality : 0.043 0.252 3672 Planarity : 0.003 0.044 4113 Dihedral : 12.607 88.045 3572 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.95 % Favored : 90.01 % Rotamer: Outliers : 3.16 % Allowed : 16.36 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.16), residues: 2873 helix: 0.60 (0.19), residues: 832 sheet: -0.98 (0.26), residues: 425 loop : -2.07 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 138 TYR 0.014 0.001 TYR B 804 PHE 0.018 0.001 PHE B 321 TRP 0.010 0.001 TRP A 539 HIS 0.007 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24183) covalent geometry : angle 0.57056 / 0.30 (32763) hydrogen bonds : bond 0.03925 / 2.59 ( 753) hydrogen bonds : angle 4.62774 / 3.22 ( 2075) metal coordination : bond 0.00348 / 0.17 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 207 time to evaluate : 0.871 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: A 370 LYS cc_start: 0.6855 (mmpt) cc_final: 0.5561 (tptp) REVERT: A 371 MET cc_start: 0.5063 (mmm) cc_final: 0.4733 (mmm) REVERT: A 417 THR cc_start: 0.4405 (OUTLIER) cc_final: 0.3976 (t) REVERT: A 420 LYS cc_start: 0.5570 (OUTLIER) cc_final: 0.4635 (mmtm) REVERT: A 788 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8128 (p0) REVERT: A 858 MET cc_start: 0.8675 (mtp) cc_final: 0.8435 (mtp) REVERT: A 981 MET cc_start: 0.7867 (ptt) cc_final: 0.7446 (ppp) REVERT: A 1006 MET cc_start: 0.7932 (mtm) cc_final: 0.7402 (mtm) REVERT: A 1028 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7969 (pp) REVERT: A 1048 ILE cc_start: 0.9240 (mt) cc_final: 0.8952 (mt) REVERT: B 68 MET cc_start: 0.7297 (tpt) cc_final: 0.6594 (ptp) REVERT: B 339 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8080 (pttm) REVERT: B 392 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8843 (ptt90) REVERT: B 495 TYR cc_start: 0.3359 (OUTLIER) cc_final: 0.3056 (t80) REVERT: B 902 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8088 (mtp85) REVERT: B 1040 MET cc_start: 0.6548 (mtm) cc_final: 0.6143 (mtp) REVERT: C 201 MET cc_start: 0.8480 (tpt) cc_final: 0.8023 (mmm) REVERT: C 204 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7686 (pp) REVERT: E 189 GLN cc_start: 0.7783 (mt0) cc_final: 0.6927 (mm110) REVERT: E 197 ASP cc_start: 0.7804 (t70) cc_final: 0.7512 (t0) REVERT: F 92 GLU cc_start: 0.8053 (mp0) cc_final: 0.7675 (mp0) REVERT: F 102 MET cc_start: 0.8167 (tmm) cc_final: 0.7855 (tmm) REVERT: H 30 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8126 (tp) REVERT: H 40 PHE cc_start: 0.7521 (t80) cc_final: 0.7221 (t80) REVERT: H 41 MET cc_start: 0.8034 (tpp) cc_final: 0.7761 (mmm) REVERT: H 46 ASN cc_start: 0.7532 (t0) cc_final: 0.7221 (t0) REVERT: H 141 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8286 (tm) REVERT: K 97 GLU cc_start: 0.8581 (tp30) cc_final: 0.8374 (tt0) REVERT: K 108 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8776 (mm-30) REVERT: L 43 ARG cc_start: 0.8579 (tpt-90) cc_final: 0.8335 (tpt170) outliers start: 81 outliers final: 61 residues processed: 270 average time/residue: 0.1531 time to fit residues: 65.1737 Evaluate side-chains 269 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 937 VAL Chi-restraints excluded: chain B residue 972 LYS Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 103 SER Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 280 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 116 optimal weight: 0.0050 chunk 207 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 HIS ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.113542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080577 restraints weight = 53492.891| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.11 r_work: 0.3023 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24190 Z= 0.109 Angle : 0.562 9.193 32763 Z= 0.299 Chirality : 0.042 0.239 3672 Planarity : 0.003 0.043 4113 Dihedral : 12.516 88.333 3572 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.68 % Favored : 90.29 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2873 helix: 0.72 (0.19), residues: 833 sheet: -0.94 (0.26), residues: 427 loop : -1.99 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1018 TYR 0.016 0.001 TYR A 362 PHE 0.015 0.001 PHE B 321 TRP 0.011 0.001 TRP A 539 HIS 0.007 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (24183) covalent geometry : angle 0.56234 / 0.30 (32763) hydrogen bonds : bond 0.03545 / 2.34 ( 753) hydrogen bonds : angle 4.52048 / 3.14 ( 2075) metal coordination : bond 0.00332 / 0.17 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6919 (mmpt) cc_final: 0.5662 (tptp) REVERT: A 371 MET cc_start: 0.5047 (mmm) cc_final: 0.4702 (mmm) REVERT: A 420 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4559 (mmtm) REVERT: A 788 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8102 (p0) REVERT: A 858 MET cc_start: 0.8650 (mtp) cc_final: 0.8413 (mtp) REVERT: A 981 MET cc_start: 0.7882 (ptt) cc_final: 0.7430 (ppp) REVERT: A 1006 MET cc_start: 0.7926 (mtm) cc_final: 0.7334 (mtm) REVERT: A 1028 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7920 (pp) REVERT: A 1048 ILE cc_start: 0.9217 (mt) cc_final: 0.8951 (mt) REVERT: B 68 MET cc_start: 0.7304 (tpt) cc_final: 0.6501 (ptp) REVERT: B 339 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8082 (pttm) REVERT: B 392 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8876 (ptt90) REVERT: B 495 TYR cc_start: 0.3338 (OUTLIER) cc_final: 0.3020 (t80) REVERT: B 902 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: B 1040 MET cc_start: 0.6552 (mtm) cc_final: 0.6126 (mtp) REVERT: C 201 MET cc_start: 0.8488 (tpt) cc_final: 0.8027 (mmm) REVERT: C 204 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7712 (pp) REVERT: E 86 ARG cc_start: 0.5062 (tmt170) cc_final: 0.4558 (tmm160) REVERT: E 189 GLN cc_start: 0.7807 (mt0) cc_final: 0.6819 (mm110) REVERT: E 197 ASP cc_start: 0.7833 (t70) cc_final: 0.7545 (t0) REVERT: F 92 GLU cc_start: 0.8045 (mp0) cc_final: 0.7692 (mp0) REVERT: F 102 MET cc_start: 0.8150 (tmm) cc_final: 0.7835 (tmm) REVERT: H 30 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8112 (tp) REVERT: H 40 PHE cc_start: 0.7497 (t80) cc_final: 0.7195 (t80) REVERT: H 41 MET cc_start: 0.8060 (tpp) cc_final: 0.7760 (mmm) REVERT: H 46 ASN cc_start: 0.7400 (t0) cc_final: 0.7137 (t0) REVERT: H 141 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (tm) REVERT: K 108 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8778 (mm-30) REVERT: L 22 LYS cc_start: 0.7527 (tptp) cc_final: 0.7173 (tppt) REVERT: L 43 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8340 (tpt170) outliers start: 65 outliers final: 50 residues processed: 259 average time/residue: 0.1695 time to fit residues: 69.3274 Evaluate side-chains 261 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 775 HIS Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 272 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 ASN B 492 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 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 = 0.3811 r_free = 0.3811 target = 0.112116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078972 restraints weight = 53657.046| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.28 r_work: 0.2976 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24190 Z= 0.169 Angle : 0.593 8.367 32763 Z= 0.315 Chirality : 0.044 0.211 3672 Planarity : 0.004 0.043 4113 Dihedral : 12.510 87.843 3567 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.69 % Allowed : 17.10 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2873 helix: 0.70 (0.19), residues: 835 sheet: -0.95 (0.26), residues: 427 loop : -2.01 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 512 TYR 0.028 0.001 TYR B 353 PHE 0.021 0.001 PHE B 321 TRP 0.014 0.001 TRP B 510 HIS 0.006 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (24183) covalent geometry : angle 0.59252 / 0.32 (32763) hydrogen bonds : bond 0.04063 / 2.69 ( 753) hydrogen bonds : angle 4.59546 / 3.19 ( 2075) metal coordination : bond 0.00469 / 0.24 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5746 Ramachandran restraints generated. 2873 Oldfield, 0 Emsley, 2873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.6836 (mmpt) cc_final: 0.5548 (tptp) REVERT: A 371 MET cc_start: 0.5086 (mmm) cc_final: 0.4741 (mmm) REVERT: A 420 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.4764 (mmtm) REVERT: A 788 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8168 (p0) REVERT: A 858 MET cc_start: 0.8695 (mtp) cc_final: 0.8454 (mtp) REVERT: A 981 MET cc_start: 0.7943 (ptt) cc_final: 0.7486 (ppp) REVERT: A 1006 MET cc_start: 0.7949 (mtm) cc_final: 0.7356 (mtm) REVERT: A 1028 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7937 (pp) REVERT: B 68 MET cc_start: 0.7261 (tpt) cc_final: 0.6546 (ptp) REVERT: B 297 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6894 (p0) REVERT: B 339 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8091 (pttm) REVERT: B 350 LEU cc_start: 0.6479 (tp) cc_final: 0.6249 (tp) REVERT: B 392 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8860 (ptt90) REVERT: B 495 TYR cc_start: 0.3597 (OUTLIER) cc_final: 0.3219 (t80) REVERT: B 902 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8143 (mtp85) REVERT: B 1040 MET cc_start: 0.6547 (mtm) cc_final: 0.6108 (mtp) REVERT: C 201 MET cc_start: 0.8529 (tpt) cc_final: 0.8077 (mmm) REVERT: C 204 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7706 (pp) REVERT: E 86 ARG cc_start: 0.5164 (tmt170) cc_final: 0.4651 (tmm160) REVERT: E 189 GLN cc_start: 0.7804 (mt0) cc_final: 0.6932 (mm110) REVERT: E 197 ASP cc_start: 0.7884 (t70) cc_final: 0.7594 (t0) REVERT: F 92 GLU cc_start: 0.8074 (mp0) cc_final: 0.7683 (mp0) REVERT: F 102 MET cc_start: 0.8148 (tmm) cc_final: 0.7825 (tmm) REVERT: H 30 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8073 (tp) REVERT: H 40 PHE cc_start: 0.7462 (t80) cc_final: 0.7126 (t80) REVERT: H 41 MET cc_start: 0.8089 (tpp) cc_final: 0.7864 (mmm) REVERT: H 46 ASN cc_start: 0.7438 (t0) cc_final: 0.7146 (t0) REVERT: H 141 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (tm) REVERT: K 108 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8778 (mm-30) REVERT: L 6 GLU cc_start: 0.5946 (mt-10) cc_final: 0.4921 (tp30) outliers start: 69 outliers final: 52 residues processed: 256 average time/residue: 0.1639 time to fit residues: 65.9325 Evaluate side-chains 260 residues out of total 2564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1028 ILE Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1082 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 84 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 902 ARG Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 972 LYS Chi-restraints excluded: chain B residue 1047 PHE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 230 TRP Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 15 CYS Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 72 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 229 optimal weight: 0.0980 chunk 264 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 273 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 HIS B 242 ASN H 42 HIS I 31 ASN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080854 restraints weight = 53300.342| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.79 r_work: 0.3028 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24190 Z= 0.115 Angle : 0.573 11.900 32763 Z= 0.303 Chirality : 0.042 0.192 3672 Planarity : 0.003 0.043 4113 Dihedral : 12.465 88.157 3567 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.54 % Allowed : 17.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.16), residues: 2873 helix: 0.83 (0.19), residues: 833 sheet: -0.89 (0.26), residues: 427 loop : -1.95 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 512 TYR 0.024 0.001 TYR B 353 PHE 0.015 0.001 PHE B 321 TRP 0.012 0.001 TRP A 539 HIS 0.007 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (24183) covalent geometry : angle 0.57285 / 0.30 (32763) hydrogen bonds : bond 0.03551 / 2.35 ( 753) hydrogen bonds : angle 4.49906 / 3.13 ( 2075) metal coordination : bond 0.00320 / 0.16 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5047.97 seconds wall clock time: 87 minutes 24.75 seconds (5244.75 seconds total)