Starting phenix.real_space_refine on Mon Jun 23 12:55:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd1_51241/06_2025/9gd1_51241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd1_51241/06_2025/9gd1_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_51241/06_2025/9gd1_51241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd1_51241/06_2025/9gd1_51241.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd1_51241/06_2025/9gd1_51241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd1_51241/06_2025/9gd1_51241.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.26, per 1000 atoms: 0.55 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: 6.36 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 11.79 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: 24.49 Time building geometry restraints manager: 7.45 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: 41018 2.87 - 5.75: 511 5.75 - 8.62: 4 8.62 - 11.49: 3 11.49 - 14.36: 3 Bond angle restraints: 41539 Sorted by residual: angle pdb=" O3' DT J 74 " pdb=" C3' DT J 74 " pdb=" C2' DT J 74 " ideal model delta sigma weight residual 111.50 101.87 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" O3' DC J 76 " pdb=" C3' DC J 76 " pdb=" C2' DC J 76 " ideal model delta sigma weight residual 111.50 102.76 8.74 1.50e+00 4.44e-01 3.39e+01 angle pdb=" O3' DC J 75 " pdb=" C3' DC J 75 " pdb=" C2' DC J 75 " ideal model delta sigma weight residual 111.50 102.81 8.69 1.50e+00 4.44e-01 3.36e+01 angle pdb=" O3' DC I-130 " pdb=" C3' DC I-130 " pdb=" C2' DC I-130 " ideal model delta sigma weight residual 111.50 104.06 7.44 1.50e+00 4.44e-01 2.46e+01 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 ... (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 - 0.049: 3118 0.049 - 0.099: 1097 0.099 - 0.148: 440 0.148 - 0.197: 29 0.197 - 0.247: 8 Chirality restraints: 4692 Sorted by residual: chirality pdb=" C3' DT J 74 " pdb=" C4' DT J 74 " pdb=" O3' DT J 74 " pdb=" C2' DT J 74 " both_signs ideal model delta sigma weight residual False -2.66 -2.91 0.25 2.00e-01 2.50e+01 1.52e+00 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 2.35 -2.10 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3' DA J 26 " pdb=" C4' DA J 26 " pdb=" O3' DA J 26 " pdb=" C2' DA J 26 " both_signs ideal model delta sigma weight residual False -2.66 -2.90 0.24 2.00e-01 2.50e+01 1.39e+00 ... (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: 27.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 77.950 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.120 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.006 0.415 29112 Z= 0.334 Angle : 0.825 14.365 41539 Z= 0.521 Chirality : 0.056 0.247 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 TRP 0.020 0.005 TRP W 447 HIS 0.013 0.003 HIS W 224 PHE 0.017 0.002 PHE W 389 TYR 0.026 0.005 TYR W1151 ARG 0.025 0.003 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.11430 ( 1703) hydrogen bonds : angle 5.38057 ( 4355) covalent geometry : bond 0.00499 (29111) covalent geometry : angle 0.82474 (41539) Misc. bond : bond 0.41519 ( 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 : 2.348 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: 0.8692 (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: 0.9264 (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: 0.4191 time to fit residues: 252.8478 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 : 2.202 ------------------------------------------------------------------------------- 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 214 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** M 31 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 = 0.2917 r_free = 0.2917 target = 0.031558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.022143 restraints weight = 304319.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.022803 restraints weight = 152558.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023236 restraints weight = 98489.008| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 29112 Z= 0.266 Angle : 0.727 8.224 41539 Z= 0.424 Chirality : 0.038 0.219 4692 Planarity : 0.005 0.056 3474 Dihedral : 29.243 173.601 7994 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.26 % Allowed : 12.07 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2054 helix: 1.14 (0.14), residues: 1331 sheet: 1.00 (0.53), residues: 92 loop : -0.44 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 417 HIS 0.010 0.001 HIS L 75 PHE 0.018 0.002 PHE W 389 TYR 0.022 0.002 TYR B 88 ARG 0.007 0.001 ARG W 807 Details of bonding type rmsd hydrogen bonds : bond 0.06129 ( 1703) hydrogen bonds : angle 4.12496 ( 4355) covalent geometry : bond 0.00592 (29111) covalent geometry : angle 0.72660 (41539) Misc. bond : bond 0.00027 ( 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 315 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 3.081 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: A 105 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8902 (mm-30) REVERT: A 120 MET cc_start: 0.8446 (mmm) cc_final: 0.8108 (mmm) REVERT: B 53 GLU cc_start: 0.9378 (mp0) cc_final: 0.9154 (pm20) REVERT: B 92 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8644 (ttp-170) REVERT: B 93 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8855 (mm-40) REVERT: C 95 LYS cc_start: 0.9827 (ttmt) cc_final: 0.9591 (tmtt) REVERT: D 68 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9446 (tm-30) REVERT: D 110 GLU cc_start: 0.9751 (OUTLIER) cc_final: 0.9547 (tt0) REVERT: E 51 ILE cc_start: 0.9690 (mt) cc_final: 0.9352 (mm) REVERT: E 64 LYS cc_start: 0.9343 (mtmt) cc_final: 0.8935 (pttm) REVERT: F 44 LYS cc_start: 0.9538 (tttt) cc_final: 0.8979 (ttmm) REVERT: F 64 ASN cc_start: 0.9470 (m-40) cc_final: 0.8918 (m-40) REVERT: F 84 MET cc_start: 0.9588 (mmp) cc_final: 0.8960 (tpp) REVERT: G 39 TYR cc_start: 0.9431 (m-80) cc_final: 0.9205 (m-80) REVERT: G 56 GLU cc_start: 0.9361 (tt0) cc_final: 0.8916 (mt-10) REVERT: G 90 ASP cc_start: 0.8802 (t0) cc_final: 0.8420 (t70) REVERT: G 91 GLU cc_start: 0.9399 (pm20) cc_final: 0.9062 (pm20) REVERT: H 48 ASP cc_start: 0.9341 (m-30) cc_final: 0.9079 (p0) REVERT: H 65 ASP cc_start: 0.9034 (t70) cc_final: 0.8645 (t70) REVERT: H 110 GLU cc_start: 0.9632 (tp30) cc_final: 0.9347 (tp30) REVERT: K 65 LEU cc_start: 0.9489 (mp) cc_final: 0.9234 (mt) REVERT: K 68 GLN cc_start: 0.8989 (pp30) cc_final: 0.8772 (pp30) REVERT: K 74 ILE cc_start: 0.9772 (mm) cc_final: 0.9561 (tt) REVERT: K 103 LEU cc_start: 0.9835 (tp) cc_final: 0.9603 (tt) REVERT: K 124 ILE cc_start: 0.9806 (mp) cc_final: 0.9438 (mp) REVERT: L 53 GLU cc_start: 0.9245 (tp30) cc_final: 0.9031 (tt0) REVERT: L 68 ASP cc_start: 0.9089 (m-30) cc_final: 0.8824 (t0) REVERT: N 113 LYS cc_start: 0.9632 (tmtt) cc_final: 0.9347 (tptt) REVERT: O 65 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9327 (mm) REVERT: O 120 MET cc_start: 0.9056 (tpp) cc_final: 0.8847 (tpt) REVERT: P 25 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8228 (t0) REVERT: P 63 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8986 (tm-30) REVERT: W 387 MET cc_start: 0.9279 (mtp) cc_final: 0.9056 (ttm) REVERT: W 403 MET cc_start: 0.8703 (mtm) cc_final: 0.8451 (mtm) REVERT: W 720 MET cc_start: 0.8644 (mpp) cc_final: 0.8177 (mpp) REVERT: W 1028 LEU cc_start: 0.9843 (pt) cc_final: 0.9470 (mt) outliers start: 41 outliers final: 22 residues processed: 299 average time/residue: 0.3989 time to fit residues: 195.6772 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 : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 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 41 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 112 GLN Chi-restraints excluded: chain O residue 65 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 Chi-restraints excluded: chain W residue 1031 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 190 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN G 24 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.033263 restraints weight = 355758.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034051 restraints weight = 139265.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.034549 restraints weight = 75538.489| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29112 Z= 0.192 Angle : 0.624 10.569 41539 Z= 0.367 Chirality : 0.035 0.196 4692 Planarity : 0.004 0.051 3474 Dihedral : 29.209 162.240 7988 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.70 % Allowed : 13.01 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2054 helix: 1.53 (0.14), residues: 1337 sheet: 0.90 (0.52), residues: 94 loop : -0.35 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 417 HIS 0.008 0.001 HIS L 75 PHE 0.015 0.001 PHE O 67 TYR 0.020 0.001 TYR H 39 ARG 0.006 0.000 ARG N 96 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 1703) hydrogen bonds : angle 3.78083 ( 4355) covalent geometry : bond 0.00422 (29111) covalent geometry : angle 0.62403 (41539) Misc. bond : bond 0.00059 ( 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 311 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 2.298 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: A 93 GLN cc_start: 0.9609 (OUTLIER) cc_final: 0.9114 (tm-30) REVERT: A 120 MET cc_start: 0.8922 (mmm) cc_final: 0.8337 (mmm) REVERT: B 84 MET cc_start: 0.9267 (mmm) cc_final: 0.9044 (mmm) REVERT: B 92 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8402 (ttp80) REVERT: B 93 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8884 (mm-40) REVERT: B 100 PHE cc_start: 0.8587 (m-80) cc_final: 0.8333 (m-80) REVERT: C 94 ASN cc_start: 0.9689 (t0) cc_final: 0.9290 (m-40) REVERT: C 95 LYS cc_start: 0.9816 (ttmt) cc_final: 0.9583 (tmtt) REVERT: D 68 GLU cc_start: 0.9651 (tm-30) cc_final: 0.9401 (tm-30) REVERT: D 96 ARG cc_start: 0.9538 (tpp80) cc_final: 0.9105 (tpp80) REVERT: E 64 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9011 (pttt) REVERT: E 97 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8663 (mt-10) REVERT: E 120 MET cc_start: 0.9375 (tpp) cc_final: 0.9112 (tpp) REVERT: F 44 LYS cc_start: 0.9513 (tttt) cc_final: 0.8941 (ttmm) REVERT: F 63 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8651 (pp20) REVERT: F 64 ASN cc_start: 0.9428 (m-40) cc_final: 0.8838 (m-40) REVERT: F 84 MET cc_start: 0.9567 (mmp) cc_final: 0.8965 (tpp) REVERT: G 56 GLU cc_start: 0.9388 (tt0) cc_final: 0.8943 (mt-10) REVERT: G 75 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9060 (mmtm) REVERT: G 101 THR cc_start: 0.9545 (m) cc_final: 0.9108 (p) REVERT: H 39 TYR cc_start: 0.9338 (m-80) cc_final: 0.9034 (m-80) REVERT: H 48 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.9059 (p0) REVERT: H 65 ASP cc_start: 0.8915 (t70) cc_final: 0.8614 (t0) REVERT: H 110 GLU cc_start: 0.9601 (tp30) cc_final: 0.9354 (tp30) REVERT: K 65 LEU cc_start: 0.9446 (mp) cc_final: 0.9101 (mp) REVERT: K 68 GLN cc_start: 0.8975 (pp30) cc_final: 0.8768 (pp30) REVERT: K 81 ASP cc_start: 0.8591 (p0) cc_final: 0.8356 (m-30) REVERT: K 93 GLN cc_start: 0.9451 (tp40) cc_final: 0.8887 (mm-40) REVERT: K 103 LEU cc_start: 0.9833 (tp) cc_final: 0.9615 (tt) REVERT: K 120 MET cc_start: 0.8777 (mmm) cc_final: 0.8554 (mmm) REVERT: K 124 ILE cc_start: 0.9806 (mp) cc_final: 0.9130 (mp) REVERT: L 53 GLU cc_start: 0.9249 (tp30) cc_final: 0.8961 (tt0) REVERT: L 59 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8848 (tptm) REVERT: L 63 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: L 68 ASP cc_start: 0.9124 (m-30) cc_final: 0.8805 (t0) REVERT: M 61 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8688 (mm-30) REVERT: M 73 ASN cc_start: 0.9097 (t0) cc_final: 0.8766 (t0) REVERT: N 42 LEU cc_start: 0.9862 (tt) cc_final: 0.9626 (pp) REVERT: N 68 GLU cc_start: 0.9255 (tt0) cc_final: 0.9020 (tm-30) REVERT: N 113 LYS cc_start: 0.9635 (tmtt) cc_final: 0.9349 (tptt) REVERT: O 93 GLN cc_start: 0.9432 (tp40) cc_final: 0.9138 (mm110) REVERT: O 94 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8387 (mm-30) REVERT: P 25 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8388 (t0) REVERT: P 63 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8967 (tm-30) REVERT: P 84 MET cc_start: 0.9536 (mmm) cc_final: 0.9279 (mmm) REVERT: W 403 MET cc_start: 0.8742 (mtm) cc_final: 0.8471 (mtm) REVERT: W 444 PHE cc_start: 0.9761 (OUTLIER) cc_final: 0.9393 (t80) REVERT: W 457 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8824 (mpp) REVERT: W 723 MET cc_start: 0.9270 (tpp) cc_final: 0.8872 (tpp) REVERT: W 837 MET cc_start: 0.9511 (tpp) cc_final: 0.9046 (tpt) REVERT: W 1028 LEU cc_start: 0.9846 (pt) cc_final: 0.9410 (mt) REVERT: W 1056 MET cc_start: 0.8957 (mmm) cc_final: 0.8712 (mmm) outliers start: 49 outliers final: 18 residues processed: 290 average time/residue: 0.4368 time to fit residues: 208.8455 Evaluate side-chains 256 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 110 CYS 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 D residue 87 THR Chi-restraints excluded: chain D residue 103 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 K residue 125 GLN Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 49 VAL 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 700 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 807 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 118 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 812 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.031695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.022228 restraints weight = 297994.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.022799 restraints weight = 153217.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.023164 restraints weight = 100035.105| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29112 Z= 0.190 Angle : 0.609 11.241 41539 Z= 0.356 Chirality : 0.035 0.217 4692 Planarity : 0.004 0.055 3474 Dihedral : 28.983 148.107 7987 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.48 % Allowed : 14.22 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2054 helix: 1.58 (0.14), residues: 1339 sheet: 0.45 (0.50), residues: 105 loop : -0.29 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 417 HIS 0.007 0.001 HIS L 75 PHE 0.017 0.001 PHE W 389 TYR 0.024 0.001 TYR W1053 ARG 0.009 0.000 ARG M 42 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1703) hydrogen bonds : angle 3.69259 ( 4355) covalent geometry : bond 0.00420 (29111) covalent geometry : angle 0.60917 (41539) Misc. bond : bond 0.00076 ( 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 304 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 2.318 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: A 93 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9091 (pp30) REVERT: A 120 MET cc_start: 0.8930 (mmm) cc_final: 0.8597 (mmm) REVERT: B 93 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8855 (mm-40) REVERT: C 56 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8949 (pp20) REVERT: C 94 ASN cc_start: 0.9642 (t0) cc_final: 0.9280 (m-40) REVERT: C 95 LYS cc_start: 0.9816 (ttmt) cc_final: 0.9611 (tmtt) REVERT: D 68 GLU cc_start: 0.9673 (tm-30) cc_final: 0.9426 (tm-30) REVERT: D 96 ARG cc_start: 0.9496 (tpp80) cc_final: 0.9183 (tpp80) REVERT: D 98 LEU cc_start: 0.9659 (tp) cc_final: 0.9393 (tt) REVERT: E 64 LYS cc_start: 0.9416 (mtmt) cc_final: 0.8850 (pttt) REVERT: E 120 MET cc_start: 0.9435 (tpp) cc_final: 0.9114 (tpt) REVERT: F 44 LYS cc_start: 0.9498 (tttt) cc_final: 0.8915 (ttmm) REVERT: F 64 ASN cc_start: 0.9495 (m-40) cc_final: 0.9253 (m-40) REVERT: F 84 MET cc_start: 0.9594 (mmp) cc_final: 0.8962 (tpp) REVERT: G 56 GLU cc_start: 0.9368 (tt0) cc_final: 0.8933 (mt-10) REVERT: G 101 THR cc_start: 0.9555 (m) cc_final: 0.9107 (p) REVERT: H 48 ASP cc_start: 0.9281 (m-30) cc_final: 0.9054 (p0) REVERT: H 65 ASP cc_start: 0.8923 (t70) cc_final: 0.8702 (t70) REVERT: H 110 GLU cc_start: 0.9592 (tp30) cc_final: 0.9363 (tp30) REVERT: K 65 LEU cc_start: 0.9491 (mp) cc_final: 0.9127 (mp) REVERT: K 93 GLN cc_start: 0.9506 (tp40) cc_final: 0.8450 (mm-40) REVERT: K 94 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8666 (mm-30) REVERT: K 97 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8566 (mt-10) REVERT: K 103 LEU cc_start: 0.9839 (tp) cc_final: 0.9638 (tt) REVERT: L 49 LEU cc_start: 0.9440 (mt) cc_final: 0.8738 (mp) REVERT: L 52 GLU cc_start: 0.8892 (pm20) cc_final: 0.8555 (pm20) REVERT: M 73 ASN cc_start: 0.9024 (t0) cc_final: 0.8686 (t0) REVERT: M 92 GLU cc_start: 0.8488 (pm20) cc_final: 0.8030 (pm20) REVERT: N 42 LEU cc_start: 0.9855 (tt) cc_final: 0.9635 (pp) REVERT: N 113 LYS cc_start: 0.9628 (tmtt) cc_final: 0.9357 (tptt) REVERT: P 25 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8500 (t0) REVERT: P 63 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8978 (tm-30) REVERT: P 84 MET cc_start: 0.9515 (mmm) cc_final: 0.9232 (mmm) REVERT: W 403 MET cc_start: 0.8802 (mtm) cc_final: 0.8583 (mtm) REVERT: W 444 PHE cc_start: 0.9724 (OUTLIER) cc_final: 0.9392 (t80) REVERT: W 1056 MET cc_start: 0.9128 (mmm) cc_final: 0.8821 (mmm) REVERT: W 1134 LEU cc_start: 0.9495 (pp) cc_final: 0.9276 (mt) outliers start: 45 outliers final: 22 residues processed: 288 average time/residue: 0.3764 time to fit residues: 177.1163 Evaluate side-chains 252 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE 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 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 49 VAL 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 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 84 PHE Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 700 LEU Chi-restraints excluded: chain W residue 754 ILE Chi-restraints excluded: chain W residue 807 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 246 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 172 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 46 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS O 108 ASN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.031315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.022042 restraints weight = 305196.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.022690 restraints weight = 154678.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.023107 restraints weight = 100337.099| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29112 Z= 0.213 Angle : 0.626 11.699 41539 Z= 0.361 Chirality : 0.035 0.242 4692 Planarity : 0.004 0.054 3474 Dihedral : 28.931 136.446 7987 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.92 % Allowed : 15.93 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2054 helix: 1.54 (0.14), residues: 1351 sheet: 0.39 (0.48), residues: 105 loop : -0.36 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 417 HIS 0.009 0.001 HIS L 75 PHE 0.010 0.001 PHE W 389 TYR 0.029 0.001 TYR B 88 ARG 0.007 0.000 ARG W 423 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 1703) hydrogen bonds : angle 3.73775 ( 4355) covalent geometry : bond 0.00469 (29111) covalent geometry : angle 0.62574 (41539) Misc. bond : bond 0.00172 ( 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 302 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 2.946 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: 0.9435 (OUTLIER) cc_final: 0.9224 (pp30) REVERT: A 94 GLU cc_start: 0.9545 (tp30) cc_final: 0.9342 (tp30) REVERT: A 120 MET cc_start: 0.8930 (mmm) cc_final: 0.8670 (mmm) REVERT: B 93 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8758 (mm-40) REVERT: C 56 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: C 64 GLU cc_start: 0.9261 (tp30) cc_final: 0.8881 (tp30) REVERT: C 90 ASP cc_start: 0.8532 (t70) cc_final: 0.8236 (t70) REVERT: C 95 LYS cc_start: 0.9821 (ttmt) cc_final: 0.9611 (tmtt) REVERT: D 68 GLU cc_start: 0.9693 (tm-30) cc_final: 0.9445 (tm-30) REVERT: D 73 GLU cc_start: 0.9532 (tp30) cc_final: 0.9267 (tp30) REVERT: D 98 LEU cc_start: 0.9648 (tp) cc_final: 0.9439 (tt) REVERT: E 64 LYS cc_start: 0.9418 (mtmt) cc_final: 0.8891 (pttt) REVERT: E 94 GLU cc_start: 0.9182 (tt0) cc_final: 0.8800 (tt0) REVERT: E 97 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8694 (mt-10) REVERT: E 120 MET cc_start: 0.9415 (tpp) cc_final: 0.9179 (tpp) REVERT: F 44 LYS cc_start: 0.9516 (tttt) cc_final: 0.8909 (ttmm) REVERT: F 64 ASN cc_start: 0.9548 (m-40) cc_final: 0.9316 (m-40) REVERT: F 84 MET cc_start: 0.9641 (mmp) cc_final: 0.8997 (tpp) REVERT: G 56 GLU cc_start: 0.9371 (tt0) cc_final: 0.8911 (mt-10) REVERT: G 101 THR cc_start: 0.9570 (m) cc_final: 0.9135 (p) REVERT: H 34 TYR cc_start: 0.9275 (m-80) cc_final: 0.9065 (m-80) REVERT: H 48 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8980 (p0) REVERT: H 65 ASP cc_start: 0.8907 (t70) cc_final: 0.8689 (t70) REVERT: H 96 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.8894 (ttm110) REVERT: H 110 GLU cc_start: 0.9628 (tp30) cc_final: 0.9390 (tp30) REVERT: K 93 GLN cc_start: 0.9485 (tp40) cc_final: 0.8399 (mm-40) REVERT: K 94 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8736 (mm-30) REVERT: K 97 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8609 (mt-10) REVERT: K 120 MET cc_start: 0.8977 (mmm) cc_final: 0.8768 (mmm) REVERT: K 124 ILE cc_start: 0.9822 (mt) cc_final: 0.9455 (mp) REVERT: L 63 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8812 (pm20) REVERT: M 73 ASN cc_start: 0.8992 (t0) cc_final: 0.8678 (t0) REVERT: N 42 LEU cc_start: 0.9854 (tt) cc_final: 0.9637 (pp) REVERT: N 68 GLU cc_start: 0.9273 (tt0) cc_final: 0.8978 (tm-30) REVERT: O 90 MET cc_start: 0.9368 (ptp) cc_final: 0.8859 (ptp) REVERT: O 94 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8578 (mm-30) REVERT: P 25 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8590 (t0) REVERT: P 63 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8981 (tm-30) REVERT: P 84 MET cc_start: 0.9544 (mmm) cc_final: 0.9275 (mmm) REVERT: P 88 TYR cc_start: 0.9212 (m-80) cc_final: 0.8861 (m-80) REVERT: W 403 MET cc_start: 0.8831 (mtm) cc_final: 0.8544 (mtm) REVERT: W 444 PHE cc_start: 0.9746 (OUTLIER) cc_final: 0.9424 (t80) REVERT: W 445 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8857 (pp20) REVERT: W 1028 LEU cc_start: 0.9782 (pt) cc_final: 0.9350 (mt) REVERT: W 1056 MET cc_start: 0.9175 (mmm) cc_final: 0.8819 (mmm) outliers start: 53 outliers final: 26 residues processed: 284 average time/residue: 0.7368 time to fit residues: 349.9556 Evaluate side-chains 260 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 103 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 46 HIS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 107 THR 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 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 84 PHE Chi-restraints excluded: chain P residue 25 ASN Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain W residue 318 GLU Chi-restraints excluded: chain W residue 375 GLU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 445 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 219 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 25 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.022803 restraints weight = 302203.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.023416 restraints weight = 150893.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.023799 restraints weight = 95837.282| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29112 Z= 0.156 Angle : 0.612 13.415 41539 Z= 0.349 Chirality : 0.034 0.204 4692 Planarity : 0.004 0.055 3474 Dihedral : 28.810 127.922 7987 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.15 % Allowed : 17.92 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2054 helix: 1.57 (0.14), residues: 1349 sheet: 0.50 (0.49), residues: 104 loop : -0.33 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 311 HIS 0.023 0.001 HIS D 46 PHE 0.014 0.001 PHE K 84 TYR 0.023 0.001 TYR B 88 ARG 0.008 0.000 ARG O 129 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1703) hydrogen bonds : angle 3.58216 ( 4355) covalent geometry : bond 0.00336 (29111) covalent geometry : angle 0.61199 (41539) Misc. bond : bond 0.00050 ( 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 298 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 2.357 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: 0.9448 (tt0) cc_final: 0.9048 (pp30) REVERT: A 120 MET cc_start: 0.8942 (mmm) cc_final: 0.8738 (mmm) REVERT: B 93 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8747 (mm-40) REVERT: C 56 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: C 90 ASP cc_start: 0.8489 (t70) cc_final: 0.8211 (t70) REVERT: C 95 LYS cc_start: 0.9806 (ttmt) cc_final: 0.9563 (tmmt) REVERT: D 68 GLU cc_start: 0.9670 (tm-30) cc_final: 0.9418 (tm-30) REVERT: D 73 GLU cc_start: 0.9481 (tp30) cc_final: 0.9217 (tp30) REVERT: D 90 GLU cc_start: 0.8980 (mp0) cc_final: 0.8647 (mp0) REVERT: D 98 LEU cc_start: 0.9653 (tp) cc_final: 0.9448 (tt) REVERT: E 64 LYS cc_start: 0.9423 (mtmt) cc_final: 0.8853 (pttt) REVERT: E 90 MET cc_start: 0.9408 (mmp) cc_final: 0.9186 (mtm) REVERT: E 94 GLU cc_start: 0.9124 (tt0) cc_final: 0.8750 (tt0) REVERT: E 97 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8677 (mt-10) REVERT: E 120 MET cc_start: 0.9403 (tpp) cc_final: 0.9181 (tpp) REVERT: F 44 LYS cc_start: 0.9484 (tttt) cc_final: 0.8918 (ttmm) REVERT: F 53 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8774 (tm-30) REVERT: F 64 ASN cc_start: 0.9512 (m-40) cc_final: 0.9162 (m110) REVERT: F 84 MET cc_start: 0.9584 (mmp) cc_final: 0.8973 (tpp) REVERT: G 56 GLU cc_start: 0.9377 (tt0) cc_final: 0.8986 (tt0) REVERT: G 95 LYS cc_start: 0.9503 (tmmt) cc_final: 0.9298 (tmmt) REVERT: G 101 THR cc_start: 0.9562 (m) cc_final: 0.9122 (p) REVERT: G 104 GLN cc_start: 0.9318 (mt0) cc_final: 0.9114 (mp10) REVERT: H 34 TYR cc_start: 0.9265 (m-80) cc_final: 0.8904 (m-80) REVERT: H 48 ASP cc_start: 0.9270 (OUTLIER) cc_final: 0.9020 (p0) REVERT: H 65 ASP cc_start: 0.8926 (t70) cc_final: 0.8692 (t70) REVERT: H 96 ARG cc_start: 0.9276 (mmm-85) cc_final: 0.8849 (ttm110) REVERT: H 110 GLU cc_start: 0.9577 (tp30) cc_final: 0.9357 (tp30) REVERT: K 93 GLN cc_start: 0.9463 (tp40) cc_final: 0.8292 (mm-40) REVERT: K 94 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8755 (mm-30) REVERT: K 97 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8554 (mt-10) REVERT: K 103 LEU cc_start: 0.9779 (tt) cc_final: 0.9411 (tp) REVERT: K 106 ASP cc_start: 0.8924 (m-30) cc_final: 0.8546 (p0) REVERT: K 120 MET cc_start: 0.8836 (mmm) cc_final: 0.8620 (mmm) REVERT: L 68 ASP cc_start: 0.9073 (m-30) cc_final: 0.8796 (t0) REVERT: M 73 ASN cc_start: 0.8921 (t0) cc_final: 0.8587 (t0) REVERT: N 42 LEU cc_start: 0.9839 (tt) cc_final: 0.9600 (pp) REVERT: O 90 MET cc_start: 0.9326 (ptp) cc_final: 0.8822 (ptp) REVERT: P 25 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8603 (t0) REVERT: P 63 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8946 (tm-30) REVERT: P 88 TYR cc_start: 0.9161 (m-80) cc_final: 0.8926 (m-80) REVERT: W 403 MET cc_start: 0.8839 (mtm) cc_final: 0.8535 (mtm) REVERT: W 444 PHE cc_start: 0.9685 (OUTLIER) cc_final: 0.9429 (t80) REVERT: W 1028 LEU cc_start: 0.9752 (pt) cc_final: 0.9278 (mt) REVERT: W 1056 MET cc_start: 0.9212 (mmm) cc_final: 0.8829 (mmm) outliers start: 39 outliers final: 19 residues processed: 284 average time/residue: 0.3694 time to fit residues: 171.3497 Evaluate side-chains 258 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 97 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 98 LEU 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 P residue 82 THR Chi-restraints excluded: chain W residue 318 GLU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 701 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 30 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 108 ASN ** M 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 254 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.032075 restraints weight = 360581.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032804 restraints weight = 141975.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033265 restraints weight = 78353.746| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 29112 Z= 0.228 Angle : 0.637 11.274 41539 Z= 0.366 Chirality : 0.036 0.303 4692 Planarity : 0.004 0.055 3474 Dihedral : 28.798 113.730 7987 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.37 % Allowed : 18.69 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2054 helix: 1.59 (0.14), residues: 1343 sheet: 0.41 (0.49), residues: 104 loop : -0.35 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 417 HIS 0.007 0.001 HIS L 75 PHE 0.008 0.001 PHE O 67 TYR 0.022 0.001 TYR D 118 ARG 0.006 0.000 ARG M 77 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 1703) hydrogen bonds : angle 3.76752 ( 4355) covalent geometry : bond 0.00502 (29111) covalent geometry : angle 0.63729 (41539) Misc. bond : bond 0.00156 ( 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 276 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 2.200 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: 0.9570 (tt0) cc_final: 0.9247 (tm-30) REVERT: A 120 MET cc_start: 0.8986 (mmm) cc_final: 0.8773 (mmm) REVERT: B 93 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8721 (mm-40) REVERT: C 56 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8852 (tt0) REVERT: C 64 GLU cc_start: 0.9260 (tp30) cc_final: 0.9057 (tp30) REVERT: C 90 ASP cc_start: 0.8567 (t70) cc_final: 0.8272 (t70) REVERT: C 95 LYS cc_start: 0.9803 (ttmt) cc_final: 0.9593 (tmtt) REVERT: D 46 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (m170) REVERT: D 68 GLU cc_start: 0.9654 (tm-30) cc_final: 0.9433 (tm-30) REVERT: D 73 GLU cc_start: 0.9528 (tp30) cc_final: 0.9304 (tp30) REVERT: D 96 ARG cc_start: 0.9541 (tpp80) cc_final: 0.9297 (tpp80) REVERT: D 98 LEU cc_start: 0.9670 (tp) cc_final: 0.9460 (tt) REVERT: E 64 LYS cc_start: 0.9408 (mtmt) cc_final: 0.8840 (pttt) REVERT: E 120 MET cc_start: 0.9373 (tpp) cc_final: 0.9102 (tpt) REVERT: F 44 LYS cc_start: 0.9521 (tttt) cc_final: 0.8973 (ttmm) REVERT: F 64 ASN cc_start: 0.9496 (m-40) cc_final: 0.9252 (m-40) REVERT: F 84 MET cc_start: 0.9592 (mmp) cc_final: 0.8966 (tpp) REVERT: G 56 GLU cc_start: 0.9349 (tt0) cc_final: 0.8960 (tt0) REVERT: G 95 LYS cc_start: 0.9555 (tmmt) cc_final: 0.9329 (tmmt) REVERT: G 101 THR cc_start: 0.9590 (m) cc_final: 0.9151 (p) REVERT: H 34 TYR cc_start: 0.9329 (m-80) cc_final: 0.8923 (m-80) REVERT: H 48 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.9044 (p0) REVERT: H 65 ASP cc_start: 0.8879 (t70) cc_final: 0.8598 (t70) REVERT: H 96 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.8881 (ttm110) REVERT: H 110 GLU cc_start: 0.9583 (tp30) cc_final: 0.9381 (tp30) REVERT: K 93 GLN cc_start: 0.9482 (tp40) cc_final: 0.9041 (tp40) REVERT: K 120 MET cc_start: 0.8750 (mmm) cc_final: 0.8514 (mmm) REVERT: L 68 ASP cc_start: 0.9032 (m-30) cc_final: 0.8769 (t0) REVERT: M 73 ASN cc_start: 0.8910 (t0) cc_final: 0.8597 (t0) REVERT: N 42 LEU cc_start: 0.9842 (tt) cc_final: 0.9618 (pp) REVERT: N 56 MET cc_start: 0.9506 (tpp) cc_final: 0.8863 (mmm) REVERT: O 67 PHE cc_start: 0.9557 (t80) cc_final: 0.9216 (t80) REVERT: O 94 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8614 (mt-10) REVERT: P 25 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8610 (t0) REVERT: P 63 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8939 (tm-30) REVERT: P 84 MET cc_start: 0.9400 (mmm) cc_final: 0.9103 (mmm) REVERT: P 88 TYR cc_start: 0.9213 (m-80) cc_final: 0.8892 (m-80) REVERT: W 444 PHE cc_start: 0.9730 (OUTLIER) cc_final: 0.9444 (t80) REVERT: W 538 MET cc_start: 0.8571 (tpp) cc_final: 0.8352 (tpp) REVERT: W 802 MET cc_start: 0.9398 (ptp) cc_final: 0.9150 (mtm) REVERT: W 1056 MET cc_start: 0.9276 (mmm) cc_final: 0.8848 (mmm) REVERT: W 1057 MET cc_start: 0.9386 (ptp) cc_final: 0.9123 (ptp) outliers start: 43 outliers final: 30 residues processed: 260 average time/residue: 0.3843 time to fit residues: 164.2262 Evaluate side-chains 254 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 108 ASN 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 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 86 ILE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 84 PHE 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 318 GLU Chi-restraints excluded: chain W residue 327 ILE Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 445 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 232 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 108 ASN K 93 GLN M 94 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032765 restraints weight = 360036.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033530 restraints weight = 140751.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.034001 restraints weight = 76949.168| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 29112 Z= 0.172 Angle : 0.626 12.770 41539 Z= 0.356 Chirality : 0.035 0.255 4692 Planarity : 0.004 0.055 3474 Dihedral : 28.799 106.777 7987 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.32 % Allowed : 18.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2054 helix: 1.59 (0.14), residues: 1343 sheet: 0.37 (0.49), residues: 104 loop : -0.36 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 311 HIS 0.018 0.001 HIS D 46 PHE 0.013 0.001 PHE W 414 TYR 0.022 0.001 TYR W1053 ARG 0.004 0.000 ARG M 77 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1703) hydrogen bonds : angle 3.69641 ( 4355) covalent geometry : bond 0.00378 (29111) covalent geometry : angle 0.62581 (41539) Misc. bond : bond 0.00096 ( 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 276 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 2.252 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: 0.9561 (tt0) cc_final: 0.9241 (tm-30) REVERT: A 120 MET cc_start: 0.8986 (mmm) cc_final: 0.8775 (mmm) REVERT: B 93 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8687 (mm-40) REVERT: C 56 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: C 90 ASP cc_start: 0.8512 (t70) cc_final: 0.8147 (t70) REVERT: C 95 LYS cc_start: 0.9798 (ttmt) cc_final: 0.9580 (tmtt) REVERT: D 68 GLU cc_start: 0.9650 (tm-30) cc_final: 0.9397 (tm-30) REVERT: D 73 GLU cc_start: 0.9518 (tp30) cc_final: 0.9299 (tp30) REVERT: D 96 ARG cc_start: 0.9513 (tpp80) cc_final: 0.9205 (tpp80) REVERT: E 64 LYS cc_start: 0.9380 (mtmt) cc_final: 0.8801 (pttt) REVERT: E 120 MET cc_start: 0.9364 (tpp) cc_final: 0.9080 (tpp) REVERT: F 44 LYS cc_start: 0.9516 (tttt) cc_final: 0.8968 (ttmm) REVERT: F 64 ASN cc_start: 0.9524 (m-40) cc_final: 0.9263 (m110) REVERT: F 84 MET cc_start: 0.9578 (mmp) cc_final: 0.8969 (tpp) REVERT: G 56 GLU cc_start: 0.9351 (tt0) cc_final: 0.8933 (tt0) REVERT: G 95 LYS cc_start: 0.9575 (tmmt) cc_final: 0.9329 (tmmt) REVERT: G 101 THR cc_start: 0.9598 (m) cc_final: 0.9161 (p) REVERT: H 34 TYR cc_start: 0.9324 (m-80) cc_final: 0.8921 (m-80) REVERT: H 48 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.9030 (p0) REVERT: H 65 ASP cc_start: 0.8813 (t70) cc_final: 0.8592 (t70) REVERT: H 96 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.8866 (ttm110) REVERT: H 110 GLU cc_start: 0.9577 (tp30) cc_final: 0.9371 (tp30) REVERT: K 93 GLN cc_start: 0.9443 (tp-100) cc_final: 0.8899 (mm-40) REVERT: K 103 LEU cc_start: 0.9799 (tp) cc_final: 0.9256 (tt) REVERT: K 106 ASP cc_start: 0.8867 (m-30) cc_final: 0.8503 (p0) REVERT: K 120 MET cc_start: 0.8749 (mmm) cc_final: 0.8521 (mmm) REVERT: L 63 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8795 (mp0) REVERT: L 68 ASP cc_start: 0.9016 (m-30) cc_final: 0.8769 (t0) REVERT: M 73 ASN cc_start: 0.8875 (t0) cc_final: 0.8554 (t0) REVERT: N 42 LEU cc_start: 0.9849 (tt) cc_final: 0.9576 (pp) REVERT: N 56 MET cc_start: 0.9482 (tpp) cc_final: 0.9061 (mmm) REVERT: N 68 GLU cc_start: 0.9235 (tt0) cc_final: 0.8829 (tm-30) REVERT: O 67 PHE cc_start: 0.9526 (t80) cc_final: 0.9179 (t80) REVERT: O 94 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8800 (mm-30) REVERT: P 25 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8613 (t0) REVERT: P 63 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8928 (tm-30) REVERT: P 84 MET cc_start: 0.9358 (mmm) cc_final: 0.9065 (mmm) REVERT: P 88 TYR cc_start: 0.9185 (m-80) cc_final: 0.8878 (m-80) REVERT: W 403 MET cc_start: 0.8943 (mtm) cc_final: 0.8678 (mtm) REVERT: W 444 PHE cc_start: 0.9722 (OUTLIER) cc_final: 0.9455 (t80) REVERT: W 720 MET cc_start: 0.8868 (mpp) cc_final: 0.8554 (mpp) REVERT: W 723 MET cc_start: 0.9314 (tpp) cc_final: 0.9088 (tpp) REVERT: W 802 MET cc_start: 0.9408 (ptp) cc_final: 0.9114 (ptp) REVERT: W 1056 MET cc_start: 0.9269 (mmm) cc_final: 0.8918 (mmm) outliers start: 42 outliers final: 27 residues processed: 260 average time/residue: 0.3565 time to fit residues: 152.6606 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 : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 107 THR 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 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 86 ILE Chi-restraints excluded: chain N residue 98 LEU 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 P residue 82 THR Chi-restraints excluded: chain W residue 318 GLU Chi-restraints excluded: chain W residue 429 ILE Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 699 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 217 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 253 optimal weight: 50.0000 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 0.0060 chunk 79 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033990 restraints weight = 352371.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.034770 restraints weight = 136764.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035252 restraints weight = 74614.069| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29112 Z= 0.146 Angle : 0.641 14.251 41539 Z= 0.357 Chirality : 0.035 0.220 4692 Planarity : 0.004 0.056 3474 Dihedral : 28.538 97.909 7987 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.76 % Allowed : 19.40 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2054 helix: 1.52 (0.14), residues: 1348 sheet: 0.32 (0.49), residues: 104 loop : -0.36 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 311 HIS 0.007 0.001 HIS L 75 PHE 0.012 0.001 PHE F 61 TYR 0.020 0.001 TYR D 118 ARG 0.004 0.000 ARG N 96 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 1703) hydrogen bonds : angle 3.65447 ( 4355) covalent geometry : bond 0.00311 (29111) covalent geometry : angle 0.64080 (41539) Misc. bond : bond 0.00022 ( 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 280 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9506 (tt0) cc_final: 0.9232 (tm-30) REVERT: A 120 MET cc_start: 0.8997 (mmm) cc_final: 0.8770 (mmm) REVERT: B 63 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9053 (mp0) REVERT: B 93 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8585 (mm-40) REVERT: C 56 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8864 (tt0) REVERT: C 64 GLU cc_start: 0.9304 (tp30) cc_final: 0.9081 (tp30) REVERT: C 90 ASP cc_start: 0.8484 (t70) cc_final: 0.8196 (t70) REVERT: C 95 LYS cc_start: 0.9786 (ttmt) cc_final: 0.9573 (tmtt) REVERT: D 68 GLU cc_start: 0.9634 (tm-30) cc_final: 0.9375 (tm-30) REVERT: E 64 LYS cc_start: 0.9400 (mtmt) cc_final: 0.8954 (pttt) REVERT: E 90 MET cc_start: 0.9287 (mtm) cc_final: 0.9035 (mmp) REVERT: E 97 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8625 (mt-10) REVERT: E 120 MET cc_start: 0.9335 (tpp) cc_final: 0.9064 (tpp) REVERT: F 44 LYS cc_start: 0.9513 (tttt) cc_final: 0.8974 (ttmm) REVERT: F 64 ASN cc_start: 0.9559 (m-40) cc_final: 0.9146 (m-40) REVERT: F 84 MET cc_start: 0.9557 (mmp) cc_final: 0.9128 (mmm) REVERT: G 56 GLU cc_start: 0.9343 (tt0) cc_final: 0.8959 (tt0) REVERT: G 95 LYS cc_start: 0.9594 (tmmt) cc_final: 0.9326 (tmmt) REVERT: G 101 THR cc_start: 0.9586 (m) cc_final: 0.9147 (p) REVERT: G 104 GLN cc_start: 0.9338 (mt0) cc_final: 0.9084 (mp10) REVERT: H 34 TYR cc_start: 0.9282 (m-80) cc_final: 0.8870 (m-80) REVERT: H 48 ASP cc_start: 0.9242 (m-30) cc_final: 0.9025 (p0) REVERT: H 65 ASP cc_start: 0.8797 (t70) cc_final: 0.8579 (t70) REVERT: H 96 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8778 (ttm110) REVERT: H 110 GLU cc_start: 0.9559 (tp30) cc_final: 0.9357 (tp30) REVERT: K 93 GLN cc_start: 0.9382 (tp40) cc_final: 0.8353 (mm-40) REVERT: K 97 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8528 (mt-10) REVERT: K 103 LEU cc_start: 0.9788 (tp) cc_final: 0.9255 (tt) REVERT: K 106 ASP cc_start: 0.8835 (m-30) cc_final: 0.8543 (p0) REVERT: K 120 MET cc_start: 0.8572 (mmm) cc_final: 0.8315 (mmm) REVERT: L 53 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8228 (mt-10) REVERT: L 68 ASP cc_start: 0.8973 (m-30) cc_final: 0.8767 (t0) REVERT: M 73 ASN cc_start: 0.8751 (t0) cc_final: 0.8451 (t0) REVERT: N 56 MET cc_start: 0.9409 (tpp) cc_final: 0.8740 (mmm) REVERT: N 68 GLU cc_start: 0.9181 (tt0) cc_final: 0.8778 (tm-30) REVERT: O 94 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8647 (mm-30) REVERT: P 25 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8709 (t0) REVERT: P 63 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8920 (tm-30) REVERT: P 84 MET cc_start: 0.9332 (mmm) cc_final: 0.9071 (mmm) REVERT: P 88 TYR cc_start: 0.9130 (m-80) cc_final: 0.8850 (m-80) REVERT: W 387 MET cc_start: 0.9550 (ptm) cc_final: 0.9317 (tmm) REVERT: W 403 MET cc_start: 0.8914 (mtm) cc_final: 0.8616 (mtm) REVERT: W 444 PHE cc_start: 0.9693 (OUTLIER) cc_final: 0.9453 (t80) REVERT: W 720 MET cc_start: 0.8899 (mpp) cc_final: 0.8594 (mpp) REVERT: W 723 MET cc_start: 0.9303 (tpp) cc_final: 0.9055 (tpp) REVERT: W 1056 MET cc_start: 0.9256 (mmm) cc_final: 0.8848 (mmm) REVERT: W 1057 MET cc_start: 0.9446 (ptp) cc_final: 0.9170 (ptp) outliers start: 32 outliers final: 20 residues processed: 268 average time/residue: 0.3753 time to fit residues: 164.5967 Evaluate side-chains 248 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 97 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 98 LEU Chi-restraints excluded: chain O residue 39 HIS 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 701 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 240 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 232 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN M 31 HIS ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.033591 restraints weight = 353666.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.034364 restraints weight = 138933.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.034846 restraints weight = 76050.575| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29112 Z= 0.159 Angle : 0.650 12.155 41539 Z= 0.364 Chirality : 0.036 0.264 4692 Planarity : 0.004 0.055 3474 Dihedral : 28.498 95.577 7987 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.21 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2054 helix: 1.49 (0.14), residues: 1348 sheet: 0.52 (0.51), residues: 98 loop : -0.35 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 311 HIS 0.009 0.001 HIS W 661 PHE 0.018 0.001 PHE N 67 TYR 0.020 0.001 TYR D 118 ARG 0.004 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 1703) hydrogen bonds : angle 3.68638 ( 4355) covalent geometry : bond 0.00347 (29111) covalent geometry : angle 0.65036 (41539) Misc. bond : bond 0.00042 ( 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 254 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 2.127 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: 0.9435 (tt0) cc_final: 0.9203 (tm-30) REVERT: B 63 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9063 (mp0) REVERT: B 92 ARG cc_start: 0.9263 (mmm-85) cc_final: 0.8955 (tpt-90) REVERT: C 56 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: C 64 GLU cc_start: 0.9290 (tp30) cc_final: 0.8817 (tp30) REVERT: C 90 ASP cc_start: 0.8516 (t70) cc_final: 0.8168 (t70) REVERT: C 95 LYS cc_start: 0.9784 (ttmt) cc_final: 0.9564 (tmmt) REVERT: D 46 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.8171 (m170) REVERT: D 68 GLU cc_start: 0.9639 (tm-30) cc_final: 0.9391 (tm-30) REVERT: E 64 LYS cc_start: 0.9432 (mtmt) cc_final: 0.8974 (pttt) REVERT: E 90 MET cc_start: 0.9280 (mtm) cc_final: 0.9027 (mmp) REVERT: E 120 MET cc_start: 0.9332 (tpp) cc_final: 0.9035 (tpp) REVERT: F 44 LYS cc_start: 0.9529 (tttt) cc_final: 0.8996 (ttmm) REVERT: F 84 MET cc_start: 0.9565 (mmp) cc_final: 0.9142 (mmm) REVERT: G 56 GLU cc_start: 0.9350 (tt0) cc_final: 0.8931 (tt0) REVERT: G 95 LYS cc_start: 0.9588 (tmmt) cc_final: 0.9311 (tmmt) REVERT: G 101 THR cc_start: 0.9604 (m) cc_final: 0.9161 (p) REVERT: G 104 GLN cc_start: 0.9351 (mt0) cc_final: 0.9102 (mp10) REVERT: H 34 TYR cc_start: 0.9258 (m-80) cc_final: 0.8823 (m-80) REVERT: H 48 ASP cc_start: 0.9254 (m-30) cc_final: 0.9029 (p0) REVERT: K 93 GLN cc_start: 0.9413 (tp-100) cc_final: 0.8984 (tp40) REVERT: K 103 LEU cc_start: 0.9796 (tp) cc_final: 0.9264 (tt) REVERT: K 106 ASP cc_start: 0.8688 (m-30) cc_final: 0.8441 (p0) REVERT: K 120 MET cc_start: 0.8668 (mmm) cc_final: 0.8403 (mmm) REVERT: L 68 ASP cc_start: 0.9017 (m-30) cc_final: 0.8774 (t0) REVERT: M 73 ASN cc_start: 0.8745 (t0) cc_final: 0.8456 (t0) REVERT: N 56 MET cc_start: 0.9435 (tpp) cc_final: 0.8795 (mmm) REVERT: N 68 GLU cc_start: 0.9229 (tt0) cc_final: 0.8807 (tm-30) REVERT: O 94 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8762 (mm-30) REVERT: P 23 ARG cc_start: 0.8905 (tpm170) cc_final: 0.8389 (mpp-170) REVERT: P 25 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8520 (t0) REVERT: P 63 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8919 (tm-30) REVERT: W 403 MET cc_start: 0.8966 (mtm) cc_final: 0.8684 (mtm) REVERT: W 444 PHE cc_start: 0.9679 (OUTLIER) cc_final: 0.9465 (t80) REVERT: W 720 MET cc_start: 0.8865 (mpp) cc_final: 0.8605 (mpp) REVERT: W 723 MET cc_start: 0.9313 (tpp) cc_final: 0.8930 (tpp) REVERT: W 802 MET cc_start: 0.9438 (ptp) cc_final: 0.9155 (ptp) REVERT: W 1056 MET cc_start: 0.9287 (mmm) cc_final: 0.8891 (mmm) REVERT: W 1057 MET cc_start: 0.9447 (ptp) cc_final: 0.9171 (ptp) outliers start: 22 outliers final: 17 residues processed: 249 average time/residue: 0.3772 time to fit residues: 153.0309 Evaluate side-chains 245 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 49 VAL 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 N residue 98 LEU Chi-restraints excluded: chain O residue 39 HIS 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 318 GLU Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 701 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 185 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** W 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** 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 = 0.2900 r_free = 0.2900 target = 0.030860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.021681 restraints weight = 314250.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.022318 restraints weight = 158754.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.022739 restraints weight = 102983.299| |-----------------------------------------------------------------------------| r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29112 Z= 0.273 Angle : 0.699 12.688 41539 Z= 0.394 Chirality : 0.038 0.224 4692 Planarity : 0.005 0.067 3474 Dihedral : 28.782 99.501 7987 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.32 % Allowed : 20.23 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2054 helix: 1.41 (0.14), residues: 1348 sheet: 0.32 (0.49), residues: 98 loop : -0.47 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 440 HIS 0.010 0.002 HIS L 75 PHE 0.022 0.002 PHE W 414 TYR 0.029 0.002 TYR D 80 ARG 0.020 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 1703) hydrogen bonds : angle 3.95223 ( 4355) covalent geometry : bond 0.00599 (29111) covalent geometry : angle 0.69930 (41539) Misc. bond : bond 0.00126 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9382.33 seconds wall clock time: 167 minutes 42.28 seconds (10062.28 seconds total)