Starting phenix.real_space_refine on Sun Jul 5 10:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd1_51241/07_2026/9gd1_51241.cif" } resolution = 4.0 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: 8 Type Number sf(0) Gaussians P 520 5.49 5 Mg 1 5.21 5 S 50 5.16 5 Be 1 3.05 5 C 15743 2.51 5 N 5055 2.21 5 O 6182 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27555 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 742 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 5275 Classifications: {'DNA': 259} Link IDs: {'rna3p': 258} Chain: "J" Number of atoms: 5344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 5344 Classifications: {'DNA': 259} Link IDs: {'rna3p': 258} Chain: "K" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 592 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 658 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "O" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 6969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6969 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 26, 'TRANS': 822} Chain breaks: 7 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.98, per 1000 atoms: 0.22 Number of scatterers: 27555 At special positions: 0 Unit cell: (127.602, 177.642, 181.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 520 15.00 Mg 1 11.99 F 3 9.00 O 6182 8.00 N 5055 7.00 C 15743 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 877.2 milliseconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3962 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 19 sheets defined 69.3% alpha, 5.5% beta 259 base pairs and 513 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.160A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.849A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.587A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.438A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.529A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.689A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.600A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.096A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.129A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.513A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.575A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 77 removed outlier: 3.986A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.831A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS K 110 " --> pdb=" O ASP K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.537A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 21 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 Processing helix chain 'L' and resid 82 through 97 removed outlier: 3.839A pdb=" N ARG L 95 " --> pdb=" O LYS L 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.151A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA M 69 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.548A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 34 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 Processing helix chain 'N' and resid 100 through 121 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.535A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.518A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 29 removed outlier: 3.980A pdb=" N ILE P 26 " --> pdb=" O ARG P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.704A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'W' and resid 205 through 211 Processing helix chain 'W' and resid 221 through 225 Processing helix chain 'W' and resid 229 through 234 Processing helix chain 'W' and resid 238 through 258 removed outlier: 4.004A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 284 removed outlier: 3.691A pdb=" N GLU W 280 " --> pdb=" O ARG W 276 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 331 removed outlier: 4.574A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 344 removed outlier: 3.681A pdb=" N ARG W 341 " --> pdb=" O HIS W 337 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 351 Processing helix chain 'W' and resid 377 through 393 Processing helix chain 'W' and resid 406 through 421 Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 448 Processing helix chain 'W' and resid 459 through 470 Processing helix chain 'W' and resid 491 through 503 removed outlier: 6.063A pdb=" N ALA W 500 " --> pdb=" O LEU W 496 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU W 501 " --> pdb=" O LYS W 497 " (cutoff:3.500A) Processing helix chain 'W' and resid 514 through 518 removed outlier: 3.512A pdb=" N ARG W 517 " --> pdb=" O GLU W 514 " (cutoff:3.500A) Processing helix chain 'W' and resid 523 through 531 Processing helix chain 'W' and resid 548 through 560 removed outlier: 3.521A pdb=" N LEU W 552 " --> pdb=" O ASN W 548 " (cutoff:3.500A) Processing helix chain 'W' and resid 561 through 565 Processing helix chain 'W' and resid 576 through 591 removed outlier: 3.666A pdb=" N GLU W 580 " --> pdb=" O ASP W 576 " (cutoff:3.500A) Processing helix chain 'W' and resid 598 through 603 Processing helix chain 'W' and resid 619 through 631 Processing helix chain 'W' and resid 633 through 639 removed outlier: 4.105A pdb=" N ALA W 639 " --> pdb=" O SER W 635 " (cutoff:3.500A) Processing helix chain 'W' and resid 650 through 661 removed outlier: 3.610A pdb=" N ASN W 660 " --> pdb=" O LYS W 656 " (cutoff:3.500A) Processing helix chain 'W' and resid 662 through 665 Processing helix chain 'W' and resid 667 through 674 Processing helix chain 'W' and resid 675 through 677 No H-bonds generated for 'chain 'W' and resid 675 through 677' Processing helix chain 'W' and resid 678 through 681 Processing helix chain 'W' and resid 682 through 693 Processing helix chain 'W' and resid 694 through 711 Processing helix chain 'W' and resid 720 through 735 Processing helix chain 'W' and resid 746 through 759 Processing helix chain 'W' and resid 771 through 775 Processing helix chain 'W' and resid 794 through 804 removed outlier: 3.909A pdb=" N ASP W 798 " --> pdb=" O ASN W 794 " (cutoff:3.500A) Processing helix chain 'W' and resid 825 through 844 removed outlier: 3.707A pdb=" N GLU W 831 " --> pdb=" O GLU W 827 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU W 839 " --> pdb=" O LYS W 835 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU W 840 " --> pdb=" O LYS W 836 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR W 841 " --> pdb=" O MET W 837 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA W 842 " --> pdb=" O ILE W 838 " (cutoff:3.500A) Processing helix chain 'W' and resid 1011 through 1026 Processing helix chain 'W' and resid 1031 through 1038 Processing helix chain 'W' and resid 1045 through 1072 Processing helix chain 'W' and resid 1129 through 1152 removed outlier: 4.053A pdb=" N LEU W1133 " --> pdb=" O ASN W1129 " (cutoff:3.500A) Processing helix chain 'W' and resid 1154 through 1158 Processing helix chain 'W' and resid 1176 through 1191 Processing helix chain 'W' and resid 1194 through 1201 Processing helix chain 'W' and resid 1202 through 1205 Processing helix chain 'W' and resid 1249 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.019A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.526A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.926A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.944A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.639A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'M' and resid 100 through 102 removed outlier: 7.150A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB7, first strand: chain 'W' and resid 179 through 182 removed outlier: 4.343A pdb=" N LYS W 216 " --> pdb=" O ASP W 180 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL W 182 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU W 214 " --> pdb=" O VAL W 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 287 through 298 removed outlier: 6.621A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG W 295 " --> pdb=" O GLN W 304 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN W 304 " --> pdb=" O ARG W 295 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER W 297 " --> pdb=" O THR W 302 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR W 302 " --> pdb=" O SER W 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 453 through 455 removed outlier: 6.182A pdb=" N ILE W 454 " --> pdb=" O LEU W 489 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN W 508 " --> pdb=" O ASN W 536 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET W 538 " --> pdb=" O GLN W 508 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY W 397 " --> pdb=" O ARG W 537 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE W 398 " --> pdb=" O LEU W 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 609 through 616 removed outlier: 6.500A pdb=" N VAL W 786 " --> pdb=" O TYR W 817 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU W 819 " --> pdb=" O VAL W 786 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE W 788 " --> pdb=" O LEU W 819 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N SER W 821 " --> pdb=" O ILE W 788 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU W 715 " --> pdb=" O VAL W 787 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL W 714 " --> pdb=" O PHE W 767 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU W 769 " --> pdb=" O VAL W 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE W 716 " --> pdb=" O LEU W 769 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN W 739 " --> pdb=" O LEU W 768 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N SER W 770 " --> pdb=" O GLN W 739 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU W 741 " --> pdb=" O SER W 770 " (cutoff:3.500A) 1039 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 664 hydrogen bonds 1328 hydrogen bond angles 0 basepair planarities 259 basepair parallelities 513 stacking parallelities Total time for adding SS restraints: 13.12 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7068 1.34 - 1.45: 7527 1.45 - 1.57: 13388 1.57 - 1.69: 1037 1.69 - 1.81: 91 Bond restraints: 29111 Sorted by residual: bond pdb=" N ARG W 341 " pdb=" CA ARG W 341 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 9.18e+00 bond pdb=" C LEU D 98 " pdb=" N LEU D 99 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.20e+00 bond pdb=" O3' DA I-117 " pdb=" P DA I-116 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.50e-02 4.44e+03 2.15e+00 bond pdb=" O3' DT J 128 " pdb=" P DA J 129 " ideal model delta sigma weight residual 1.607 1.585 0.022 1.50e-02 4.44e+03 2.13e+00 bond pdb=" O3' DT J 25 " pdb=" P DA J 26 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.50e-02 4.44e+03 2.05e+00 ... (remaining 29106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 41279 2.87 - 5.75: 253 5.75 - 8.62: 4 8.62 - 11.49: 0 11.49 - 14.36: 3 Bond angle restraints: 41539 Sorted by residual: angle pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 119.96 105.60 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F3 BEF W1502 " ideal model delta sigma weight residual 120.12 106.07 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " pdb=" F2 BEF W1502 " ideal model delta sigma weight residual 119.91 106.35 13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C4' DG I 20 " pdb=" O4' DG I 20 " pdb=" C1' DG I 20 " ideal model delta sigma weight residual 110.10 105.79 4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" C4' DG J 20 " pdb=" O4' DG J 20 " pdb=" C1' DG J 20 " ideal model delta sigma weight residual 110.10 106.40 3.70 1.00e+00 1.00e+00 1.37e+01 ... (remaining 41534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 13415 35.87 - 71.74: 2757 71.74 - 107.61: 18 107.61 - 143.47: 1 143.47 - 179.34: 2 Dihedral angle restraints: 16193 sinusoidal: 10074 harmonic: 6119 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.65 179.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 101.06 -161.05 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" CA LEU W 258 " pdb=" C LEU W 258 " pdb=" N ASP W 259 " pdb=" CA ASP W 259 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 16190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3326 0.047 - 0.093: 997 0.093 - 0.140: 353 0.140 - 0.186: 14 0.186 - 0.233: 2 Chirality restraints: 4692 Sorted by residual: chirality pdb=" P DG I-173 " pdb=" OP1 DG I-173 " pdb=" OP2 DG I-173 " pdb=" O5' DG I-173 " both_signs ideal model delta sigma weight residual True 2.34 -2.10 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR W1151 " pdb=" N TYR W1151 " pdb=" C TYR W1151 " pdb=" CB TYR W1151 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C4' DA I-157 " pdb=" C5' DA I-157 " pdb=" O4' DA I-157 " pdb=" C3' DA I-157 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 4689 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 55 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ARG B 55 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG B 55 " 0.023 2.00e-02 2.50e+03 pdb=" N GLY B 56 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 52 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLU B 52 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU B 52 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU B 53 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR W 443 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR W 443 " 0.057 2.00e-02 2.50e+03 pdb=" O THR W 443 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE W 444 " -0.019 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 339 2.62 - 3.19: 23724 3.19 - 3.76: 48986 3.76 - 4.33: 67275 4.33 - 4.90: 98124 Nonbonded interactions: 238448 Sorted by model distance: nonbonded pdb=" OD1 ASP W 513 " pdb="MG MG W1503 " model vdw 2.052 2.170 nonbonded pdb=" OE2 GLU W 514 " pdb="MG MG W1503 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP W 513 " pdb="MG MG W1503 " model vdw 2.117 2.170 nonbonded pdb=" CG ASP W 513 " pdb="MG MG W1503 " model vdw 2.291 2.400 nonbonded pdb=" OE2 GLU O 50 " pdb=" NE ARG P 39 " model vdw 2.311 3.120 ... (remaining 238443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 41 through 133) selection = (chain 'O' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 97) selection = (chain 'F' and resid 25 through 97) selection = (chain 'L' and resid 25 through 97) selection = (chain 'P' and resid 25 through 97) } ncs_group { reference = (chain 'C' and resid 16 through 110) selection = (chain 'G' and resid 16 through 110) selection = (chain 'M' and resid 16 through 110) } ncs_group { reference = (chain 'D' and resid 32 through 120) selection = (chain 'H' and resid 32 through 120) selection = (chain 'N' and resid 32 through 120) } 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 group one per residue 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: 7.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 37.230 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 29112 Z= 0.347 Angle : 0.696 14.365 41539 Z= 0.482 Chirality : 0.048 0.233 4692 Planarity : 0.010 0.117 3474 Dihedral : 25.612 179.344 12231 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.39 % Allowed : 6.28 % Favored : 93.33 % 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: -0.53 (0.16), residues: 2054 helix: -0.13 (0.12), residues: 1323 sheet: 0.95 (0.52), residues: 83 loop : -0.72 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG H 76 TYR 0.026 0.005 TYR W1151 PHE 0.017 0.002 PHE W 389 TRP 0.020 0.005 TRP W 447 HIS 0.013 0.003 HIS W 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.25 (29111) covalent geometry : angle 0.69624 / 0.48 (41539) hydrogen bonds : bond 0.11430 / 7.51 ( 1703) hydrogen bonds : angle 5.38057 / 3.87 ( 4355) Misc. bond : bond 0.41519 / 21.85 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 381 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.9636 (mm) cc_final: 0.9423 (tt) REVERT: A 130 ILE cc_start: 0.9425 (mm) cc_final: 0.9023 (mm) REVERT: B 85 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8740 (p0) REVERT: B 93 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8691 (mm-40) REVERT: C 95 LYS cc_start: 0.9818 (ttmt) cc_final: 0.9586 (tmtt) REVERT: D 36 ILE cc_start: 0.9576 (pt) cc_final: 0.9340 (pt) REVERT: D 68 GLU cc_start: 0.9686 (tm-30) cc_final: 0.9459 (tm-30) REVERT: E 51 ILE cc_start: 0.9656 (mt) cc_final: 0.9310 (mm) REVERT: E 64 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9111 (mtmt) REVERT: E 76 GLN cc_start: 0.9668 (tt0) cc_final: 0.9441 (tm-30) REVERT: E 130 ILE cc_start: 0.9554 (mm) cc_final: 0.9222 (mt) REVERT: F 44 LYS cc_start: 0.9492 (tttt) cc_final: 0.8938 (ttmm) REVERT: F 64 ASN cc_start: 0.9375 (m110) cc_final: 0.9105 (m-40) REVERT: F 84 MET cc_start: 0.9620 (mmp) cc_final: 0.9402 (tpp) REVERT: G 39 TYR cc_start: 0.9344 (m-80) cc_final: 0.9074 (m-80) REVERT: G 56 GLU cc_start: 0.9385 (tt0) cc_final: 0.9016 (tt0) REVERT: G 90 ASP cc_start: 0.8608 (t0) cc_final: 0.8134 (t0) REVERT: G 92 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9111 (mp0) REVERT: G 100 VAL cc_start: 0.9624 (t) cc_final: 0.9311 (p) REVERT: H 48 ASP cc_start: 0.9347 (m-30) cc_final: 0.9112 (p0) REVERT: H 65 ASP cc_start: 0.8984 (t70) cc_final: 0.8579 (t70) REVERT: H 68 GLU cc_start: 0.9432 (tt0) cc_final: 0.9154 (tm-30) REVERT: H 92 GLN cc_start: 0.9723 (tt0) cc_final: 0.9100 (tm-30) REVERT: H 110 GLU cc_start: 0.9653 (tp30) cc_final: 0.9343 (tp30) REVERT: K 65 LEU cc_start: 0.9714 (mp) cc_final: 0.8879 (mt) REVERT: K 74 ILE cc_start: 0.9863 (mm) cc_final: 0.9590 (tt) REVERT: K 90 MET cc_start: 0.9455 (mmp) cc_final: 0.9174 (mmp) REVERT: K 97 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8887 (tt0) REVERT: L 46 ILE cc_start: 0.9615 (pt) cc_final: 0.9366 (mp) REVERT: L 53 GLU cc_start: 0.9273 (tp30) cc_final: 0.8931 (tm-30) REVERT: L 63 GLU cc_start: 0.9034 (tp30) cc_final: 0.8818 (tp30) REVERT: L 93 GLN cc_start: 0.9286 (tp40) cc_final: 0.9076 (tp-100) REVERT: M 56 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8533 (mm-30) REVERT: N 113 LYS cc_start: 0.9624 (tmtt) cc_final: 0.9334 (tptt) REVERT: P 63 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8989 (tm-30) REVERT: W 387 MET cc_start: 0.9279 (mtp) cc_final: 0.9001 (ttm) REVERT: W 457 MET cc_start: 0.9006 (mtp) cc_final: 0.8710 (mtp) REVERT: W 720 MET cc_start: 0.8556 (mpp) cc_final: 0.8124 (mpp) REVERT: W 723 MET cc_start: 0.9263 (tmm) cc_final: 0.8658 (tmm) REVERT: W 1057 MET cc_start: 0.9319 (mmp) cc_final: 0.9089 (mmm) outliers start: 7 outliers final: 2 residues processed: 387 average time/residue: 0.1828 time to fit residues: 110.7012 Evaluate side-chains 234 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain W residue 407 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 overall best weight: 5.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN W 343 ASN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 520 ASN W 653 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.031299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.021913 restraints weight = 305668.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.022572 restraints weight = 153811.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.023003 restraints weight = 99204.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.023251 restraints weight = 75199.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023340 restraints weight = 62943.956| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 29112 Z= 0.262 Angle : 0.853 11.189 41539 Z= 0.469 Chirality : 0.052 0.233 4692 Planarity : 0.005 0.053 3474 Dihedral : 29.875 171.262 7994 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.37 % Allowed : 12.35 % Favored : 85.28 % 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: 0.70 (0.18), residues: 2054 helix: 0.95 (0.14), residues: 1331 sheet: 0.85 (0.50), residues: 98 loop : -0.52 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 128 TYR 0.019 0.002 TYR N 39 PHE 0.020 0.002 PHE O 67 TRP 0.013 0.002 TRP W 417 HIS 0.010 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.26 (29111) covalent geometry : angle 0.85333 / 0.47 (41539) hydrogen bonds : bond 0.07133 / 4.81 ( 1703) hydrogen bonds : angle 4.33039 / 3.12 ( 4355) Misc. bond : bond 0.00184 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8893 (mm-30) REVERT: A 120 MET cc_start: 0.8532 (mmm) cc_final: 0.8147 (mmm) REVERT: B 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8975 (mp0) REVERT: B 93 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8857 (mm-40) REVERT: C 95 LYS cc_start: 0.9830 (ttmt) cc_final: 0.9595 (tmtt) REVERT: D 68 GLU cc_start: 0.9673 (tm-30) cc_final: 0.9425 (tm-30) REVERT: D 96 ARG cc_start: 0.9512 (tpp80) cc_final: 0.9124 (tpp80) REVERT: E 51 ILE cc_start: 0.9706 (mt) cc_final: 0.9330 (mm) REVERT: E 105 GLU cc_start: 0.9546 (tm-30) cc_final: 0.9339 (tm-30) REVERT: F 44 LYS cc_start: 0.9568 (tttt) cc_final: 0.9041 (tppt) REVERT: F 64 ASN cc_start: 0.9442 (m-40) cc_final: 0.8924 (m110) REVERT: F 84 MET cc_start: 0.9580 (mmp) cc_final: 0.9000 (tpp) REVERT: G 39 TYR cc_start: 0.9453 (m-80) cc_final: 0.9186 (m-80) REVERT: G 56 GLU cc_start: 0.9354 (tt0) cc_final: 0.8888 (mt-10) REVERT: G 90 ASP cc_start: 0.8811 (t0) cc_final: 0.8514 (t70) REVERT: G 91 GLU cc_start: 0.9398 (pm20) cc_final: 0.9118 (pm20) REVERT: H 48 ASP cc_start: 0.9330 (m-30) cc_final: 0.9084 (p0) REVERT: H 56 MET cc_start: 0.9550 (tpp) cc_final: 0.9226 (mmm) REVERT: H 65 ASP cc_start: 0.9003 (t70) cc_final: 0.8620 (t70) REVERT: H 68 GLU cc_start: 0.9351 (tt0) cc_final: 0.9149 (tm-30) REVERT: H 110 GLU cc_start: 0.9638 (tp30) cc_final: 0.9356 (tp30) REVERT: K 65 LEU cc_start: 0.9512 (mp) cc_final: 0.9242 (mt) REVERT: K 74 ILE cc_start: 0.9783 (mm) cc_final: 0.9567 (tt) REVERT: K 90 MET cc_start: 0.9373 (mmp) cc_final: 0.9000 (mmp) REVERT: L 53 GLU cc_start: 0.9244 (tp30) cc_final: 0.8865 (tt0) REVERT: L 63 GLU cc_start: 0.8885 (tp30) cc_final: 0.8612 (tp30) REVERT: L 68 ASP cc_start: 0.9057 (m-30) cc_final: 0.8806 (t0) REVERT: M 89 ASN cc_start: 0.9498 (m-40) cc_final: 0.9201 (m110) REVERT: M 92 GLU cc_start: 0.8523 (mp0) cc_final: 0.8321 (pm20) REVERT: N 68 GLU cc_start: 0.9241 (tt0) cc_final: 0.8994 (tm-30) REVERT: N 113 LYS cc_start: 0.9636 (tmtt) cc_final: 0.9361 (tptt) REVERT: P 25 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8124 (t0) REVERT: P 63 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8978 (tm-30) REVERT: W 403 MET cc_start: 0.8672 (mtm) cc_final: 0.8395 (mtm) REVERT: W 720 MET cc_start: 0.8625 (mpp) cc_final: 0.8191 (mpp) REVERT: W 1028 LEU cc_start: 0.9843 (pt) cc_final: 0.9468 (mt) outliers start: 43 outliers final: 26 residues processed: 289 average time/residue: 0.1559 time to fit residues: 74.1062 Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 87 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 212 optimal weight: 0.0010 chunk 68 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K 93 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN W 339 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.033311 restraints weight = 355630.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034073 restraints weight = 137387.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.034530 restraints weight = 74243.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034886 restraints weight = 52467.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035186 restraints weight = 41823.446| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29112 Z= 0.162 Angle : 0.694 10.827 41539 Z= 0.400 Chirality : 0.048 0.395 4692 Planarity : 0.004 0.062 3474 Dihedral : 29.976 175.779 7988 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.87 % Allowed : 12.40 % Favored : 84.73 % 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: 1.19 (0.18), residues: 2054 helix: 1.39 (0.14), residues: 1329 sheet: 0.99 (0.54), residues: 92 loop : -0.42 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 77 TYR 0.016 0.002 TYR B 88 PHE 0.023 0.002 PHE W 389 TRP 0.008 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (29111) covalent geometry : angle 0.69358 / 0.40 (41539) hydrogen bonds : bond 0.04808 / 3.24 ( 1703) hydrogen bonds : angle 3.91187 / 2.84 ( 4355) Misc. bond : bond 0.00191 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9619 (OUTLIER) cc_final: 0.9328 (tm-30) REVERT: A 120 MET cc_start: 0.8942 (mmm) cc_final: 0.8520 (mmm) REVERT: B 92 ARG cc_start: 0.9360 (mmm-85) cc_final: 0.8777 (tmm-80) REVERT: B 93 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8826 (mm-40) REVERT: C 95 LYS cc_start: 0.9813 (ttmt) cc_final: 0.9588 (tmtt) REVERT: D 68 GLU cc_start: 0.9649 (tm-30) cc_final: 0.9394 (tm-30) REVERT: D 110 GLU cc_start: 0.9748 (OUTLIER) cc_final: 0.9457 (mt-10) REVERT: E 51 ILE cc_start: 0.9619 (mt) cc_final: 0.9296 (mm) REVERT: E 105 GLU cc_start: 0.9496 (tm-30) cc_final: 0.9254 (tm-30) REVERT: F 44 LYS cc_start: 0.9528 (tttt) cc_final: 0.8931 (ttmm) REVERT: F 64 ASN cc_start: 0.9445 (m-40) cc_final: 0.8682 (m-40) REVERT: F 84 MET cc_start: 0.9593 (mmp) cc_final: 0.8934 (tpp) REVERT: G 56 GLU cc_start: 0.9364 (tt0) cc_final: 0.8885 (mt-10) REVERT: G 92 GLU cc_start: 0.8935 (mp0) cc_final: 0.8691 (mp0) REVERT: G 101 THR cc_start: 0.9522 (m) cc_final: 0.9038 (p) REVERT: H 48 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (p0) REVERT: H 65 ASP cc_start: 0.9009 (t70) cc_final: 0.8541 (t0) REVERT: H 68 GLU cc_start: 0.9333 (tt0) cc_final: 0.9125 (tm-30) REVERT: H 110 GLU cc_start: 0.9618 (tp30) cc_final: 0.9327 (tp30) REVERT: K 65 LEU cc_start: 0.9406 (mp) cc_final: 0.9148 (mt) REVERT: K 74 ILE cc_start: 0.9780 (mm) cc_final: 0.9569 (tt) REVERT: K 81 ASP cc_start: 0.8539 (p0) cc_final: 0.8217 (m-30) REVERT: K 120 MET cc_start: 0.8935 (mmm) cc_final: 0.8649 (mmm) REVERT: L 53 GLU cc_start: 0.9238 (tp30) cc_final: 0.8775 (tt0) REVERT: L 68 ASP cc_start: 0.9071 (m-30) cc_final: 0.8802 (t0) REVERT: M 61 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8964 (mm-30) REVERT: N 68 GLU cc_start: 0.9261 (tt0) cc_final: 0.8999 (tm-30) REVERT: N 113 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9331 (tptt) REVERT: O 93 GLN cc_start: 0.9518 (tp40) cc_final: 0.9075 (mm-40) REVERT: O 94 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8202 (mm-30) REVERT: P 25 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8311 (t0) REVERT: P 63 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8929 (tm-30) REVERT: P 84 MET cc_start: 0.9558 (mmm) cc_final: 0.9221 (mmm) REVERT: W 403 MET cc_start: 0.8687 (mtm) cc_final: 0.8334 (mtm) REVERT: W 444 PHE cc_start: 0.9764 (OUTLIER) cc_final: 0.9382 (t80) REVERT: W 457 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8815 (mpp) REVERT: W 538 MET cc_start: 0.8768 (tpp) cc_final: 0.8528 (tpp) REVERT: W 697 MET cc_start: 0.9231 (mtm) cc_final: 0.8647 (ttm) REVERT: W 720 MET cc_start: 0.8729 (mpp) cc_final: 0.8126 (mpp) REVERT: W 1028 LEU cc_start: 0.9847 (pt) cc_final: 0.9435 (mt) outliers start: 52 outliers final: 20 residues processed: 296 average time/residue: 0.1683 time to fit residues: 81.9021 Evaluate side-chains 253 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 529 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 193 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 213 optimal weight: 0.0870 chunk 91 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS K 93 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 = 0.3050 r_free = 0.3050 target = 0.040595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033015 restraints weight = 356155.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033772 restraints weight = 139401.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034283 restraints weight = 75219.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.034666 restraints weight = 51886.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.034801 restraints weight = 41362.182| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29112 Z= 0.163 Angle : 0.680 11.043 41539 Z= 0.389 Chirality : 0.045 0.213 4692 Planarity : 0.005 0.139 3474 Dihedral : 29.861 166.409 7987 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.87 % Allowed : 13.56 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.18), residues: 2054 helix: 1.36 (0.14), residues: 1334 sheet: 0.76 (0.51), residues: 100 loop : -0.33 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.033 0.002 TYR B 88 PHE 0.030 0.001 PHE K 67 TRP 0.008 0.001 TRP W 417 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (29111) covalent geometry : angle 0.68042 / 0.39 (41539) hydrogen bonds : bond 0.04691 / 3.16 ( 1703) hydrogen bonds : angle 3.86576 / 2.82 ( 4355) Misc. bond : bond 0.00172 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9608 (tt0) cc_final: 0.9320 (tm-30) REVERT: A 120 MET cc_start: 0.8891 (mmm) cc_final: 0.8464 (mmm) REVERT: B 59 LYS cc_start: 0.9661 (tttm) cc_final: 0.9384 (tttm) REVERT: B 63 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8955 (mt-10) REVERT: B 93 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8805 (mm-40) REVERT: C 56 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9133 (tm-30) REVERT: C 95 LYS cc_start: 0.9817 (ttmt) cc_final: 0.9592 (tmtt) REVERT: D 68 GLU cc_start: 0.9645 (tm-30) cc_final: 0.9392 (tm-30) REVERT: D 110 GLU cc_start: 0.9744 (OUTLIER) cc_final: 0.9470 (mt-10) REVERT: E 50 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8901 (mm-30) REVERT: E 105 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9226 (tm-30) REVERT: E 124 ILE cc_start: 0.9600 (OUTLIER) cc_final: 0.9339 (pt) REVERT: F 44 LYS cc_start: 0.9532 (tttt) cc_final: 0.8950 (ttmm) REVERT: F 64 ASN cc_start: 0.9256 (m-40) cc_final: 0.8989 (m-40) REVERT: F 84 MET cc_start: 0.9603 (mmp) cc_final: 0.8966 (tpp) REVERT: G 56 GLU cc_start: 0.9373 (tt0) cc_final: 0.8970 (tt0) REVERT: G 101 THR cc_start: 0.9553 (m) cc_final: 0.9102 (p) REVERT: H 39 TYR cc_start: 0.9352 (m-80) cc_final: 0.9110 (m-80) REVERT: H 48 ASP cc_start: 0.9277 (m-30) cc_final: 0.9017 (p0) REVERT: H 65 ASP cc_start: 0.8995 (t70) cc_final: 0.8595 (t70) REVERT: H 110 GLU cc_start: 0.9598 (tp30) cc_final: 0.9328 (tp30) REVERT: K 74 ILE cc_start: 0.9793 (mm) cc_final: 0.9575 (tt) REVERT: K 81 ASP cc_start: 0.8580 (p0) cc_final: 0.8289 (m-30) REVERT: K 93 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9081 (tp40) REVERT: L 63 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: L 68 ASP cc_start: 0.9070 (m-30) cc_final: 0.8838 (t0) REVERT: M 89 ASN cc_start: 0.9507 (m-40) cc_final: 0.9239 (m110) REVERT: M 92 GLU cc_start: 0.8238 (pm20) cc_final: 0.7584 (pm20) REVERT: M 112 GLN cc_start: 0.7974 (mt0) cc_final: 0.7501 (mp10) REVERT: N 113 LYS cc_start: 0.9632 (tmtt) cc_final: 0.9349 (tptt) REVERT: O 94 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9039 (mm-30) REVERT: O 120 MET cc_start: 0.9192 (tpp) cc_final: 0.8817 (tpp) REVERT: P 25 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8269 (t0) REVERT: P 63 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8912 (tm-30) REVERT: P 84 MET cc_start: 0.9543 (mmm) cc_final: 0.9208 (mmm) REVERT: W 403 MET cc_start: 0.8799 (mtm) cc_final: 0.8500 (mtm) REVERT: W 444 PHE cc_start: 0.9763 (OUTLIER) cc_final: 0.9389 (t80) REVERT: W 457 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8825 (mpp) REVERT: W 538 MET cc_start: 0.8652 (tpp) cc_final: 0.8442 (tpp) REVERT: W 697 MET cc_start: 0.9262 (mtm) cc_final: 0.8677 (ttm) REVERT: W 802 MET cc_start: 0.9263 (mtm) cc_final: 0.9044 (ptp) REVERT: W 1028 LEU cc_start: 0.9844 (pt) cc_final: 0.9412 (mt) outliers start: 52 outliers final: 26 residues processed: 281 average time/residue: 0.1575 time to fit residues: 73.7759 Evaluate side-chains 257 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 781 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 27 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 204 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 172 optimal weight: 0.0170 chunk 4 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 452 ASN W 719 GLN W 812 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.022597 restraints weight = 288159.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023216 restraints weight = 146358.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023638 restraints weight = 93626.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023939 restraints weight = 70852.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.024104 restraints weight = 59216.369| |-----------------------------------------------------------------------------| r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29112 Z= 0.143 Angle : 0.651 11.706 41539 Z= 0.374 Chirality : 0.043 0.275 4692 Planarity : 0.004 0.073 3474 Dihedral : 29.749 158.830 7987 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.70 % Allowed : 14.61 % Favored : 82.69 % 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: 1.27 (0.18), residues: 2054 helix: 1.44 (0.14), residues: 1335 sheet: 0.75 (0.51), residues: 100 loop : -0.37 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.042 0.001 TYR B 88 PHE 0.032 0.001 PHE K 67 TRP 0.006 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (29111) covalent geometry : angle 0.65103 / 0.37 (41539) hydrogen bonds : bond 0.04107 / 2.76 ( 1703) hydrogen bonds : angle 3.75296 / 2.73 ( 4355) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9628 (OUTLIER) cc_final: 0.9318 (tm-30) REVERT: A 120 MET cc_start: 0.8935 (mmm) cc_final: 0.8495 (mmm) REVERT: B 93 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8731 (mm-40) REVERT: C 56 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8907 (tt0) REVERT: C 94 ASN cc_start: 0.9669 (t0) cc_final: 0.9262 (m-40) REVERT: C 95 LYS cc_start: 0.9813 (ttmt) cc_final: 0.9576 (tmtt) REVERT: D 68 GLU cc_start: 0.9667 (tm-30) cc_final: 0.9416 (tm-30) REVERT: E 94 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8974 (tt0) REVERT: E 97 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8615 (mt-10) REVERT: E 105 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9239 (tm-30) REVERT: F 44 LYS cc_start: 0.9501 (tttt) cc_final: 0.8910 (ttmm) REVERT: F 53 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8462 (tm-30) REVERT: F 64 ASN cc_start: 0.9475 (m-40) cc_final: 0.9146 (m-40) REVERT: F 84 MET cc_start: 0.9617 (mmp) cc_final: 0.8962 (tpp) REVERT: G 56 GLU cc_start: 0.9374 (tt0) cc_final: 0.8998 (tt0) REVERT: G 101 THR cc_start: 0.9538 (m) cc_final: 0.9077 (p) REVERT: H 48 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8929 (p0) REVERT: H 65 ASP cc_start: 0.8894 (t70) cc_final: 0.8582 (t70) REVERT: H 110 GLU cc_start: 0.9608 (tp30) cc_final: 0.9353 (tp30) REVERT: K 65 LEU cc_start: 0.9368 (mt) cc_final: 0.9082 (mm) REVERT: K 68 GLN cc_start: 0.8863 (pp30) cc_final: 0.8577 (pp30) REVERT: K 74 ILE cc_start: 0.9795 (mm) cc_final: 0.9576 (tt) REVERT: K 93 GLN cc_start: 0.9328 (tp40) cc_final: 0.9127 (mm-40) REVERT: K 106 ASP cc_start: 0.8975 (m-30) cc_final: 0.8645 (p0) REVERT: K 120 MET cc_start: 0.9078 (mmm) cc_final: 0.8671 (mmm) REVERT: L 63 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8778 (mp0) REVERT: L 68 ASP cc_start: 0.9091 (m-30) cc_final: 0.8844 (t0) REVERT: M 61 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8927 (mm-30) REVERT: M 73 ASN cc_start: 0.9078 (t0) cc_final: 0.8759 (t0) REVERT: M 89 ASN cc_start: 0.9533 (m-40) cc_final: 0.9273 (m110) REVERT: N 42 LEU cc_start: 0.9855 (tt) cc_final: 0.9642 (pp) REVERT: N 113 LYS cc_start: 0.9633 (tmtt) cc_final: 0.9335 (tptt) REVERT: O 94 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9068 (mm-30) REVERT: O 120 MET cc_start: 0.9266 (tpp) cc_final: 0.8808 (tpt) REVERT: P 25 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8377 (t0) REVERT: P 63 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8970 (tm-30) REVERT: P 84 MET cc_start: 0.9524 (mmm) cc_final: 0.9255 (mmm) REVERT: W 444 PHE cc_start: 0.9736 (OUTLIER) cc_final: 0.9372 (t80) REVERT: W 538 MET cc_start: 0.8667 (tpp) cc_final: 0.8425 (tpp) REVERT: W 697 MET cc_start: 0.9138 (mtm) cc_final: 0.8692 (ttm) REVERT: W 802 MET cc_start: 0.9226 (mtm) cc_final: 0.8901 (ptp) REVERT: W 837 MET cc_start: 0.9467 (tpp) cc_final: 0.9025 (tpt) REVERT: W 1134 LEU cc_start: 0.9492 (pp) cc_final: 0.9263 (mt) outliers start: 49 outliers final: 23 residues processed: 289 average time/residue: 0.1633 time to fit residues: 78.2878 Evaluate side-chains 265 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 314 LEU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 769 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 167 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 213 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 = 0.3047 r_free = 0.3047 target = 0.040376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.032818 restraints weight = 357778.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033578 restraints weight = 139350.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.034036 restraints weight = 75954.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.034449 restraints weight = 53186.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034581 restraints weight = 42122.813| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29112 Z= 0.170 Angle : 0.660 11.289 41539 Z= 0.377 Chirality : 0.043 0.293 4692 Planarity : 0.004 0.069 3474 Dihedral : 29.680 152.142 7987 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.54 % Allowed : 16.26 % Favored : 81.20 % 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: 1.31 (0.18), residues: 2054 helix: 1.52 (0.14), residues: 1334 sheet: 0.28 (0.50), residues: 105 loop : -0.38 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.037 0.001 TYR B 88 PHE 0.015 0.001 PHE W 389 TRP 0.007 0.001 TRP W 417 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (29111) covalent geometry : angle 0.66044 / 0.38 (41539) hydrogen bonds : bond 0.04378 / 2.94 ( 1703) hydrogen bonds : angle 3.78691 / 2.76 ( 4355) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: A 94 GLU cc_start: 0.9435 (tp30) cc_final: 0.9216 (tp30) REVERT: A 120 MET cc_start: 0.8983 (mmm) cc_final: 0.8656 (mmm) REVERT: B 93 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8762 (mm-40) REVERT: C 56 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9014 (pp20) REVERT: C 64 GLU cc_start: 0.9283 (tp30) cc_final: 0.8878 (tp30) REVERT: C 94 ASN cc_start: 0.9679 (t0) cc_final: 0.9277 (m-40) REVERT: C 95 LYS cc_start: 0.9813 (ttmt) cc_final: 0.9551 (ttpt) REVERT: D 68 GLU cc_start: 0.9650 (tm-30) cc_final: 0.9399 (tm-30) REVERT: D 110 GLU cc_start: 0.9717 (OUTLIER) cc_final: 0.9461 (mt-10) REVERT: E 50 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9247 (mm-30) REVERT: E 94 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8935 (tt0) REVERT: E 97 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8704 (mt-10) REVERT: E 105 GLU cc_start: 0.9489 (tm-30) cc_final: 0.9197 (tm-30) REVERT: F 44 LYS cc_start: 0.9534 (tttt) cc_final: 0.8941 (ttmm) REVERT: F 63 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8622 (pp20) REVERT: F 64 ASN cc_start: 0.9443 (m-40) cc_final: 0.8834 (m-40) REVERT: F 84 MET cc_start: 0.9616 (mmp) cc_final: 0.8995 (tpp) REVERT: G 56 GLU cc_start: 0.9368 (tt0) cc_final: 0.8982 (tt0) REVERT: G 101 THR cc_start: 0.9525 (m) cc_final: 0.9063 (p) REVERT: H 48 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8984 (p0) REVERT: H 110 GLU cc_start: 0.9602 (tp30) cc_final: 0.9359 (tp30) REVERT: K 65 LEU cc_start: 0.9401 (mt) cc_final: 0.9083 (mm) REVERT: K 68 GLN cc_start: 0.8939 (pp30) cc_final: 0.8723 (pp30) REVERT: K 74 ILE cc_start: 0.9806 (mm) cc_final: 0.9586 (tt) REVERT: L 63 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: L 68 ASP cc_start: 0.9093 (m-30) cc_final: 0.8834 (t0) REVERT: M 73 ASN cc_start: 0.9046 (t0) cc_final: 0.8728 (t0) REVERT: N 56 MET cc_start: 0.9455 (mmm) cc_final: 0.9221 (tpp) REVERT: N 113 LYS cc_start: 0.9636 (tmtt) cc_final: 0.9352 (tptt) REVERT: O 94 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9107 (mm-30) REVERT: P 25 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8359 (t0) REVERT: P 63 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8943 (tm-30) REVERT: P 84 MET cc_start: 0.9506 (mmm) cc_final: 0.9250 (mmm) REVERT: W 444 PHE cc_start: 0.9766 (OUTLIER) cc_final: 0.9412 (t80) REVERT: W 538 MET cc_start: 0.8647 (tpp) cc_final: 0.8424 (tpp) REVERT: W 802 MET cc_start: 0.9302 (mtm) cc_final: 0.8918 (mtm) REVERT: W 837 MET cc_start: 0.9479 (tpp) cc_final: 0.8982 (tpt) REVERT: W 1028 LEU cc_start: 0.9788 (pt) cc_final: 0.9352 (mt) REVERT: W 1134 LEU cc_start: 0.9495 (pp) cc_final: 0.9270 (mt) outliers start: 46 outliers final: 26 residues processed: 271 average time/residue: 0.1629 time to fit residues: 73.2658 Evaluate side-chains 259 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 38 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 127 optimal weight: 0.0170 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 = 0.2929 r_free = 0.2929 target = 0.031872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.022460 restraints weight = 292746.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.023113 restraints weight = 147744.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.023551 restraints weight = 95929.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023837 restraints weight = 73027.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.023985 restraints weight = 61366.954| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29112 Z= 0.146 Angle : 0.657 11.691 41539 Z= 0.373 Chirality : 0.043 0.321 4692 Planarity : 0.004 0.065 3474 Dihedral : 29.604 148.310 7987 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.76 % Allowed : 17.14 % Favored : 80.10 % 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: 1.26 (0.18), residues: 2054 helix: 1.48 (0.14), residues: 1335 sheet: 0.29 (0.50), residues: 105 loop : -0.38 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 423 TYR 0.031 0.001 TYR B 88 PHE 0.012 0.001 PHE W 389 TRP 0.008 0.001 TRP W 311 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (29111) covalent geometry : angle 0.65733 / 0.37 (41539) hydrogen bonds : bond 0.03932 / 2.64 ( 1703) hydrogen bonds : angle 3.71505 / 2.71 ( 4355) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9587 (tt0) cc_final: 0.9227 (tm-30) REVERT: A 120 MET cc_start: 0.8934 (mmm) cc_final: 0.8606 (mmm) REVERT: B 93 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8702 (mm-40) REVERT: C 56 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: C 64 GLU cc_start: 0.9244 (tp30) cc_final: 0.8807 (tp30) REVERT: C 94 ASN cc_start: 0.9667 (t0) cc_final: 0.9263 (m-40) REVERT: C 95 LYS cc_start: 0.9813 (ttmt) cc_final: 0.9583 (tmtt) REVERT: D 68 GLU cc_start: 0.9665 (tm-30) cc_final: 0.9418 (tm-30) REVERT: D 110 GLU cc_start: 0.9730 (OUTLIER) cc_final: 0.9516 (mt-10) REVERT: E 50 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9176 (mm-30) REVERT: E 94 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: E 97 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8687 (mt-10) REVERT: E 105 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9207 (tm-30) REVERT: F 44 LYS cc_start: 0.9513 (tttt) cc_final: 0.8916 (ttmm) REVERT: F 63 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8643 (pp20) REVERT: F 64 ASN cc_start: 0.9466 (m-40) cc_final: 0.8870 (m-40) REVERT: F 84 MET cc_start: 0.9616 (mmp) cc_final: 0.8996 (tpp) REVERT: G 56 GLU cc_start: 0.9365 (tt0) cc_final: 0.8990 (tt0) REVERT: G 101 THR cc_start: 0.9522 (m) cc_final: 0.9057 (p) REVERT: G 104 GLN cc_start: 0.9373 (mt0) cc_final: 0.9128 (mp10) REVERT: H 48 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8972 (p0) REVERT: H 110 GLU cc_start: 0.9593 (tp30) cc_final: 0.9347 (tp30) REVERT: K 65 LEU cc_start: 0.9425 (mt) cc_final: 0.9070 (mm) REVERT: K 68 GLN cc_start: 0.8932 (pp30) cc_final: 0.8696 (pp30) REVERT: K 74 ILE cc_start: 0.9805 (mm) cc_final: 0.9580 (tt) REVERT: K 106 ASP cc_start: 0.8957 (m-30) cc_final: 0.8600 (p0) REVERT: K 120 MET cc_start: 0.8638 (mmm) cc_final: 0.8382 (mmm) REVERT: L 68 ASP cc_start: 0.9108 (m-30) cc_final: 0.8866 (t0) REVERT: M 61 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8940 (mm-30) REVERT: M 73 ASN cc_start: 0.9007 (t0) cc_final: 0.8680 (t0) REVERT: O 94 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9110 (mm-30) REVERT: P 25 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8467 (t0) REVERT: P 63 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8939 (tm-30) REVERT: P 84 MET cc_start: 0.9479 (mmm) cc_final: 0.9244 (mmm) REVERT: W 444 PHE cc_start: 0.9722 (OUTLIER) cc_final: 0.9389 (t80) REVERT: W 538 MET cc_start: 0.8584 (tpp) cc_final: 0.8376 (tpp) REVERT: W 837 MET cc_start: 0.9466 (tpp) cc_final: 0.8931 (tpt) REVERT: W 1028 LEU cc_start: 0.9756 (pt) cc_final: 0.9286 (mt) outliers start: 50 outliers final: 29 residues processed: 277 average time/residue: 0.1649 time to fit residues: 76.0238 Evaluate side-chains 263 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 457 MET Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 171 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 chunk 87 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN ** W 452 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 = 0.2928 r_free = 0.2928 target = 0.031858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.022467 restraints weight = 302431.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.023131 restraints weight = 152163.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.023557 restraints weight = 98119.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.023875 restraints weight = 74485.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.024033 restraints weight = 62052.071| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29112 Z= 0.155 Angle : 0.668 15.289 41539 Z= 0.377 Chirality : 0.042 0.290 4692 Planarity : 0.004 0.061 3474 Dihedral : 29.507 142.136 7987 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.09 % Allowed : 18.47 % Favored : 79.44 % 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: 1.30 (0.18), residues: 2054 helix: 1.49 (0.14), residues: 1338 sheet: 0.26 (0.50), residues: 105 loop : -0.32 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 423 TYR 0.030 0.001 TYR B 88 PHE 0.024 0.001 PHE K 67 TRP 0.009 0.001 TRP W 311 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (29111) covalent geometry : angle 0.66814 / 0.38 (41539) hydrogen bonds : bond 0.04059 / 2.72 ( 1703) hydrogen bonds : angle 3.71846 / 2.71 ( 4355) Misc. bond : bond 0.00112 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9599 (tt0) cc_final: 0.9201 (tm-30) REVERT: A 94 GLU cc_start: 0.9507 (tp30) cc_final: 0.9267 (tp30) REVERT: A 120 MET cc_start: 0.8916 (mmm) cc_final: 0.8636 (mmm) REVERT: B 93 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8650 (mm-40) REVERT: C 56 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: C 64 GLU cc_start: 0.9238 (tp30) cc_final: 0.8827 (tp30) REVERT: C 95 LYS cc_start: 0.9805 (ttmt) cc_final: 0.9584 (tmtt) REVERT: D 56 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9365 (tpp) REVERT: D 68 GLU cc_start: 0.9681 (tm-30) cc_final: 0.9437 (tm-30) REVERT: D 110 GLU cc_start: 0.9733 (OUTLIER) cc_final: 0.9522 (mt-10) REVERT: E 50 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9241 (mm-30) REVERT: E 90 MET cc_start: 0.9418 (mmp) cc_final: 0.9192 (mtm) REVERT: E 94 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: E 97 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8709 (mt-10) REVERT: E 105 GLU cc_start: 0.9511 (tm-30) cc_final: 0.9213 (tm-30) REVERT: F 44 LYS cc_start: 0.9529 (tttt) cc_final: 0.8930 (ttmm) REVERT: F 64 ASN cc_start: 0.9485 (m-40) cc_final: 0.9256 (m-40) REVERT: F 84 MET cc_start: 0.9650 (mmp) cc_final: 0.9047 (tpp) REVERT: F 92 ARG cc_start: 0.9196 (tpt-90) cc_final: 0.8932 (tpt-90) REVERT: G 56 GLU cc_start: 0.9364 (tt0) cc_final: 0.8970 (tt0) REVERT: G 101 THR cc_start: 0.9496 (m) cc_final: 0.9021 (p) REVERT: G 104 GLN cc_start: 0.9417 (mt0) cc_final: 0.9107 (mp10) REVERT: H 48 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.9010 (p0) REVERT: H 96 ARG cc_start: 0.9303 (mmm-85) cc_final: 0.8866 (ttm110) REVERT: H 110 GLU cc_start: 0.9629 (tp30) cc_final: 0.9379 (tp30) REVERT: K 65 LEU cc_start: 0.9402 (mt) cc_final: 0.9023 (mm) REVERT: K 68 GLN cc_start: 0.8983 (pp30) cc_final: 0.8733 (pp30) REVERT: K 74 ILE cc_start: 0.9815 (mm) cc_final: 0.9569 (tt) REVERT: L 63 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: L 68 ASP cc_start: 0.9194 (m-30) cc_final: 0.8893 (t0) REVERT: M 73 ASN cc_start: 0.8969 (t0) cc_final: 0.8641 (t0) REVERT: P 25 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8460 (t0) REVERT: P 63 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8954 (tm-30) REVERT: P 84 MET cc_start: 0.9513 (mmm) cc_final: 0.9267 (mmm) REVERT: W 444 PHE cc_start: 0.9741 (OUTLIER) cc_final: 0.9426 (t80) outliers start: 38 outliers final: 25 residues processed: 262 average time/residue: 0.1704 time to fit residues: 73.5849 Evaluate side-chains 262 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 314 LEU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 148 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 214 optimal weight: 4.9990 chunk 44 optimal weight: 0.0570 chunk 223 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN W 254 GLN ** W 452 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 = 0.2910 r_free = 0.2910 target = 0.031325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.022059 restraints weight = 305160.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.022701 restraints weight = 153983.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.023144 restraints weight = 100161.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.023418 restraints weight = 75256.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.023512 restraints weight = 62969.943| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29112 Z= 0.195 Angle : 0.688 13.814 41539 Z= 0.388 Chirality : 0.042 0.273 4692 Planarity : 0.004 0.063 3474 Dihedral : 29.549 134.617 7987 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.98 % Allowed : 19.24 % Favored : 78.78 % 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: 1.27 (0.18), residues: 2054 helix: 1.47 (0.14), residues: 1341 sheet: 0.28 (0.50), residues: 105 loop : -0.35 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.019 0.001 TYR B 88 PHE 0.020 0.001 PHE K 67 TRP 0.008 0.001 TRP W 417 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.20 (29111) covalent geometry : angle 0.68786 / 0.39 (41539) hydrogen bonds : bond 0.04720 / 3.17 ( 1703) hydrogen bonds : angle 3.83471 / 2.78 ( 4355) Misc. bond : bond 0.00202 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9584 (tt0) cc_final: 0.9154 (tm-30) REVERT: A 94 GLU cc_start: 0.9482 (tp30) cc_final: 0.9128 (tp30) REVERT: A 120 MET cc_start: 0.8951 (mmm) cc_final: 0.8675 (mmm) REVERT: B 93 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8675 (mm-40) REVERT: C 56 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9007 (pp20) REVERT: C 64 GLU cc_start: 0.9262 (tp30) cc_final: 0.8875 (tp30) REVERT: C 95 LYS cc_start: 0.9812 (ttmt) cc_final: 0.9584 (tmtt) REVERT: D 56 MET cc_start: 0.9562 (OUTLIER) cc_final: 0.9353 (tpp) REVERT: D 68 GLU cc_start: 0.9682 (tm-30) cc_final: 0.9468 (tm-30) REVERT: D 73 GLU cc_start: 0.9592 (tp30) cc_final: 0.9310 (tp30) REVERT: D 110 GLU cc_start: 0.9747 (OUTLIER) cc_final: 0.9506 (mt-10) REVERT: E 90 MET cc_start: 0.9417 (mmp) cc_final: 0.9168 (mtm) REVERT: E 94 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8850 (tt0) REVERT: E 97 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8718 (mt-10) REVERT: E 105 GLU cc_start: 0.9493 (tm-30) cc_final: 0.9196 (tm-30) REVERT: F 44 LYS cc_start: 0.9531 (tttt) cc_final: 0.8962 (ttmm) REVERT: F 63 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8765 (pp20) REVERT: F 64 ASN cc_start: 0.9507 (m-40) cc_final: 0.8998 (m-40) REVERT: F 84 MET cc_start: 0.9650 (mmp) cc_final: 0.9009 (tpp) REVERT: F 92 ARG cc_start: 0.9181 (tpt-90) cc_final: 0.8957 (tpt-90) REVERT: G 56 GLU cc_start: 0.9337 (tt0) cc_final: 0.8934 (tt0) REVERT: H 48 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.9041 (p0) REVERT: H 56 MET cc_start: 0.9591 (tpp) cc_final: 0.9241 (mpp) REVERT: H 73 GLU cc_start: 0.9304 (tp30) cc_final: 0.8990 (tp30) REVERT: H 96 ARG cc_start: 0.9333 (mmm-85) cc_final: 0.8844 (ttm110) REVERT: H 110 GLU cc_start: 0.9630 (tp30) cc_final: 0.9391 (tp30) REVERT: K 65 LEU cc_start: 0.9447 (mt) cc_final: 0.9042 (mp) REVERT: K 68 GLN cc_start: 0.9038 (pp30) cc_final: 0.8819 (pp30) REVERT: K 74 ILE cc_start: 0.9828 (mm) cc_final: 0.9582 (tt) REVERT: K 120 MET cc_start: 0.8555 (mmm) cc_final: 0.8278 (mmm) REVERT: L 68 ASP cc_start: 0.9230 (m-30) cc_final: 0.8934 (t0) REVERT: M 73 ASN cc_start: 0.8968 (t0) cc_final: 0.8629 (t0) REVERT: P 25 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8564 (t0) REVERT: P 63 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8946 (tm-30) REVERT: P 84 MET cc_start: 0.9523 (mmm) cc_final: 0.9227 (mmm) REVERT: W 444 PHE cc_start: 0.9744 (OUTLIER) cc_final: 0.9429 (t80) REVERT: W 802 MET cc_start: 0.9298 (mtm) cc_final: 0.9022 (ptp) REVERT: W 1028 LEU cc_start: 0.9750 (pt) cc_final: 0.9283 (mt) REVERT: W 1057 MET cc_start: 0.9357 (ptp) cc_final: 0.9122 (ptp) outliers start: 36 outliers final: 25 residues processed: 251 average time/residue: 0.1658 time to fit residues: 68.3445 Evaluate side-chains 255 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 240 optimal weight: 3.9990 chunk 78 optimal weight: 40.0000 chunk 218 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** W 452 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 = 0.2878 r_free = 0.2878 target = 0.030383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.021279 restraints weight = 312513.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.021892 restraints weight = 157973.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.022312 restraints weight = 103007.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.022472 restraints weight = 78259.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.022691 restraints weight = 68099.329| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29112 Z= 0.269 Angle : 0.761 14.131 41539 Z= 0.424 Chirality : 0.044 0.260 4692 Planarity : 0.005 0.060 3474 Dihedral : 29.791 121.071 7987 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.93 % Allowed : 19.35 % Favored : 78.72 % 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: 0.87 (0.18), residues: 2054 helix: 1.17 (0.14), residues: 1344 sheet: 0.12 (0.50), residues: 105 loop : -0.53 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG W 834 TYR 0.022 0.002 TYR D 80 PHE 0.028 0.002 PHE K 67 TRP 0.013 0.002 TRP W 440 HIS 0.009 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.27 (29111) covalent geometry : angle 0.76083 / 0.42 (41539) hydrogen bonds : bond 0.06365 / 4.29 ( 1703) hydrogen bonds : angle 4.10200 / 2.97 ( 4355) Misc. bond : bond 0.00295 / 0.16 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9617 (tt0) cc_final: 0.9184 (tm-30) REVERT: A 94 GLU cc_start: 0.9484 (tp30) cc_final: 0.9187 (tp30) REVERT: A 120 MET cc_start: 0.9045 (mmm) cc_final: 0.8713 (mmm) REVERT: B 92 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8743 (ttp80) REVERT: B 93 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8805 (mm110) REVERT: C 56 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.8969 (pp20) REVERT: C 64 GLU cc_start: 0.9299 (tp30) cc_final: 0.8893 (tp30) REVERT: C 95 LYS cc_start: 0.9800 (ttmt) cc_final: 0.9550 (ptmt) REVERT: D 68 GLU cc_start: 0.9683 (tm-30) cc_final: 0.9473 (tm-30) REVERT: D 110 GLU cc_start: 0.9739 (OUTLIER) cc_final: 0.9293 (mt-10) REVERT: E 105 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9153 (tm-30) REVERT: F 44 LYS cc_start: 0.9533 (tttt) cc_final: 0.8986 (ttmm) REVERT: F 84 MET cc_start: 0.9627 (mmp) cc_final: 0.9187 (mmm) REVERT: G 56 GLU cc_start: 0.9322 (tt0) cc_final: 0.8905 (tt0) REVERT: H 56 MET cc_start: 0.9608 (tpp) cc_final: 0.9253 (mpp) REVERT: H 73 GLU cc_start: 0.9311 (tp30) cc_final: 0.9087 (tp30) REVERT: H 96 ARG cc_start: 0.9391 (mmm-85) cc_final: 0.8897 (ttm110) REVERT: H 110 GLU cc_start: 0.9601 (tp30) cc_final: 0.9205 (tp30) REVERT: K 74 ILE cc_start: 0.9830 (mm) cc_final: 0.9620 (tt) REVERT: K 120 MET cc_start: 0.8649 (mmm) cc_final: 0.8347 (mmm) REVERT: L 68 ASP cc_start: 0.9245 (m-30) cc_final: 0.8960 (t0) REVERT: M 73 ASN cc_start: 0.9066 (t0) cc_final: 0.8726 (t0) REVERT: M 89 ASN cc_start: 0.9569 (m-40) cc_final: 0.9306 (m110) REVERT: N 68 GLU cc_start: 0.9242 (tt0) cc_final: 0.8877 (tm-30) REVERT: P 25 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8540 (t0) REVERT: P 63 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8930 (tm-30) REVERT: P 84 MET cc_start: 0.9510 (mmm) cc_final: 0.9123 (mmm) REVERT: P 88 TYR cc_start: 0.9218 (m-80) cc_final: 0.8693 (m-80) REVERT: W 444 PHE cc_start: 0.9731 (OUTLIER) cc_final: 0.9380 (t80) REVERT: W 1028 LEU cc_start: 0.9755 (pt) cc_final: 0.9260 (mt) outliers start: 35 outliers final: 23 residues processed: 238 average time/residue: 0.1811 time to fit residues: 70.8739 Evaluate side-chains 229 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain W residue 314 LEU Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 699 LEU Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 701 ASP Chi-restraints excluded: chain W residue 754 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 181 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN O 113 HIS ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 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 = 0.2905 r_free = 0.2905 target = 0.031182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.021884 restraints weight = 306096.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.022527 restraints weight = 155346.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.022967 restraints weight = 100936.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.023250 restraints weight = 76528.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023364 restraints weight = 64254.198| |-----------------------------------------------------------------------------| r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29112 Z= 0.162 Angle : 0.704 14.754 41539 Z= 0.393 Chirality : 0.043 0.325 4692 Planarity : 0.004 0.058 3474 Dihedral : 29.746 115.912 7987 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 20.12 % Favored : 78.56 % 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: 1.07 (0.18), residues: 2054 helix: 1.32 (0.14), residues: 1342 sheet: 0.20 (0.50), residues: 104 loop : -0.44 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 96 TYR 0.020 0.001 TYR B 88 PHE 0.026 0.001 PHE K 67 TRP 0.010 0.001 TRP W 417 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (29111) covalent geometry : angle 0.70359 / 0.39 (41539) hydrogen bonds : bond 0.04296 / 2.88 ( 1703) hydrogen bonds : angle 3.89508 / 2.84 ( 4355) Misc. bond : bond 0.00152 / 0.08 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4666.45 seconds wall clock time: 81 minutes 22.80 seconds (4882.80 seconds total)