Starting phenix.real_space_refine on Mon Mar 25 06:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anc_3147/03_2024/5anc_3147.pdb" } resolution = 4.2 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= 0.003 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 1158 5.49 5 S 128 5.16 5 C 25017 2.51 5 N 8368 2.21 5 O 12136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46807 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3176 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1491 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 184} Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1571 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1245 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 150} Chain: "E" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1017 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 125} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "G" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 241} Chain: "K" Number of atoms: 8800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8800 Classifications: {'peptide': 1120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1057} Chain: "N" Number of atoms: 24758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 24758 Inner-chain residues flagged as termini: ['pdbres=" C N1356 "', 'pdbres=" A N2392 "', 'pdbres=" A N2925 "'] Classifications: {'RNA': 1162} Modifications used: {'5*END': 4, 'rna2p_pur': 109, 'rna2p_pyr': 57, 'rna3p_pur': 515, 'rna3p_pyr': 481} Link IDs: {'rna2p': 166, 'rna3p': 995} Time building chain proxies: 23.74, per 1000 atoms: 0.51 Number of scatterers: 46807 At special positions: 0 Unit cell: (206.15, 194.18, 214.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 1158 15.00 O 12136 8.00 N 8368 7.00 C 25017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 33 " distance=2.94 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.15 Conformation dependent library (CDL) restraints added in 4.5 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5216 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 31 sheets defined 26.1% alpha, 12.9% beta 321 base pairs and 519 stacking pairs defined. Time for finding SS restraints: 20.62 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.990A pdb=" N PHE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 140 through 157 removed outlier: 4.571A pdb=" N LYS A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.958A pdb=" N GLU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.764A pdb=" N GLN B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.774A pdb=" N VAL C 11 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.549A pdb=" N LEU C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.926A pdb=" N ILE C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.611A pdb=" N VAL C 100 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 77 through 86 removed outlier: 4.032A pdb=" N ILE D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.813A pdb=" N ASP D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 removed outlier: 4.335A pdb=" N MET D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 134 removed outlier: 3.718A pdb=" N ILE D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'F' and resid 62 through 73 removed outlier: 3.514A pdb=" N CYS F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 145 through 158 removed outlier: 3.647A pdb=" N GLU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.956A pdb=" N LYS F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS F 185 " --> pdb=" O TYR F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 removed outlier: 3.943A pdb=" N ASN F 217 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'G' and resid 53 through 60 removed outlier: 3.619A pdb=" N ILE G 58 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 13 removed outlier: 4.032A pdb=" N LEU H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 41 removed outlier: 4.073A pdb=" N VAL J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.553A pdb=" N ILE J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 110 Processing helix chain 'J' and resid 129 through 140 removed outlier: 4.102A pdb=" N LYS J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 163 removed outlier: 3.647A pdb=" N LYS J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.935A pdb=" N LYS J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 removed outlier: 3.566A pdb=" N ASP J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU J 227 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 228 " --> pdb=" O ILE J 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 13 removed outlier: 3.784A pdb=" N MET K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.810A pdb=" N LEU K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER K 42 " --> pdb=" O CYS K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 67 removed outlier: 3.965A pdb=" N GLN K 64 " --> pdb=" O ARG K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 108 removed outlier: 4.005A pdb=" N SER K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 135 removed outlier: 4.109A pdb=" N ALA K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 155 removed outlier: 5.236A pdb=" N LEU K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 178 removed outlier: 4.302A pdb=" N TYR K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 176 " --> pdb=" O GLN K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 3.519A pdb=" N GLN K 204 " --> pdb=" O PRO K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 256 removed outlier: 3.506A pdb=" N LYS K 255 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE K 256 " --> pdb=" O TYR K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 269 removed outlier: 3.912A pdb=" N GLY K 269 " --> pdb=" O LYS K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 296 Processing helix chain 'K' and resid 297 through 311 removed outlier: 3.624A pdb=" N ILE K 301 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 323 removed outlier: 4.167A pdb=" N ASP K 317 " --> pdb=" O LYS K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 348 removed outlier: 3.972A pdb=" N ILE K 341 " --> pdb=" O PRO K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 363 removed outlier: 3.785A pdb=" N LEU K 356 " --> pdb=" O SER K 352 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA K 357 " --> pdb=" O HIS K 353 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 371 removed outlier: 4.170A pdb=" N ILE K 369 " --> pdb=" O SER K 365 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR K 370 " --> pdb=" O PRO K 366 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA K 371 " --> pdb=" O LEU K 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 365 through 371' Processing helix chain 'K' and resid 397 through 402 removed outlier: 3.842A pdb=" N LYS K 401 " --> pdb=" O ALA K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 434 Processing helix chain 'K' and resid 434 through 445 removed outlier: 3.709A pdb=" N ILE K 438 " --> pdb=" O THR K 434 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 439 " --> pdb=" O GLN K 435 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 removed outlier: 4.428A pdb=" N LYS K 452 " --> pdb=" O ARG K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 483 removed outlier: 3.574A pdb=" N GLY K 482 " --> pdb=" O GLU K 478 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP K 483 " --> pdb=" O GLU K 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 478 through 483' Processing helix chain 'K' and resid 529 through 536 Processing helix chain 'K' and resid 626 through 628 No H-bonds generated for 'chain 'K' and resid 626 through 628' Processing helix chain 'K' and resid 629 through 644 removed outlier: 3.909A pdb=" N LEU K 633 " --> pdb=" O GLU K 629 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL K 634 " --> pdb=" O MET K 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 639 " --> pdb=" O LYS K 635 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 642 " --> pdb=" O LYS K 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 665 through 674 removed outlier: 3.605A pdb=" N LEU K 674 " --> pdb=" O CYS K 670 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 769 Processing helix chain 'K' and resid 786 through 796 removed outlier: 4.186A pdb=" N HIS K 790 " --> pdb=" O GLY K 786 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET K 791 " --> pdb=" O GLU K 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS K 793 " --> pdb=" O THR K 789 " (cutoff:3.500A) Processing helix chain 'K' and resid 806 through 812 Processing helix chain 'K' and resid 865 through 877 removed outlier: 3.685A pdb=" N ILE K 869 " --> pdb=" O LEU K 865 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER K 871 " --> pdb=" O ASN K 867 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY K 872 " --> pdb=" O SER K 868 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU K 875 " --> pdb=" O SER K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 907 through 918 Processing helix chain 'K' and resid 936 through 942 removed outlier: 3.595A pdb=" N THR K 942 " --> pdb=" O PHE K 938 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 976 removed outlier: 3.670A pdb=" N LYS K 966 " --> pdb=" O ILE K 962 " (cutoff:3.500A) Processing helix chain 'K' and resid 992 through 994 No H-bonds generated for 'chain 'K' and resid 992 through 994' Processing helix chain 'K' and resid 995 through 1006 removed outlier: 3.828A pdb=" N VAL K 999 " --> pdb=" O VAL K 995 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1044 Processing sheet with id= AA, first strand: chain 'A' and resid 329 through 333 removed outlier: 6.533A pdb=" N ILE A 72 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 57 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 74 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS A 55 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 76 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N MET A 53 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A 78 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 51 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 344 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 105 through 106 Processing sheet with id= AC, first strand: chain 'A' and resid 181 through 185 removed outlier: 7.209A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 181 through 185 removed outlier: 7.209A pdb=" N ARG A 162 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU A 89 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 164 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 218 through 223 removed outlier: 5.427A pdb=" N ILE A 218 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 222 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 278 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 229 through 230 Processing sheet with id= BA, first strand: chain 'B' and resid 8 through 11 removed outlier: 4.080A pdb=" N ARG B 8 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.591A pdb=" N ASP B 19 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.360A pdb=" N GLU B 87 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG B 182 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 89 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 176 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 101 through 104 Processing sheet with id= CA, first strand: chain 'C' and resid 86 through 90 removed outlier: 7.872A pdb=" N MET C 26 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 191 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 28 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'D' and resid 13 through 16 removed outlier: 4.032A pdb=" N PHE D 14 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 63 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'E' and resid 22 through 24 removed outlier: 6.908A pdb=" N MET E 59 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL E 39 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET E 57 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 58 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA E 99 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain 'E' and resid 85 through 86 Processing sheet with id= FA, first strand: chain 'F' and resid 134 through 139 removed outlier: 6.606A pdb=" N ILE F 134 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER F 54 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 136 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N CYS F 49 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing sheet with id= FB, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.184A pdb=" N ILE F 99 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY F 124 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id= FC, first strand: chain 'F' and resid 192 through 193 removed outlier: 3.642A pdb=" N ASN F 196 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing sheet with id= GA, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= JA, first strand: chain 'J' and resid 20 through 22 Processing sheet with id= JB, first strand: chain 'J' and resid 57 through 59 removed outlier: 7.158A pdb=" N GLN J 64 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= JC, first strand: chain 'J' and resid 195 through 197 removed outlier: 4.276A pdb=" N LYS J 195 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS J 210 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG J 175 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU J 234 " --> pdb=" O ILE J 177 " (cutoff:3.500A) Processing sheet with id= KA, first strand: chain 'K' and resid 23 through 26 removed outlier: 3.879A pdb=" N VAL K 142 " --> pdb=" O CYS K 113 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE K 115 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 144 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL K 233 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing sheet with id= KB, first strand: chain 'K' and resid 73 through 75 removed outlier: 3.667A pdb=" N SER K 73 " --> pdb=" O ASP K 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 92 " --> pdb=" O SER K 73 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE K 75 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing sheet with id= KC, first strand: chain 'K' and resid 520 through 522 removed outlier: 3.529A pdb=" N LYS K 520 " --> pdb=" O LEU K 560 " (cutoff:3.500A) Processing sheet with id= KD, first strand: chain 'K' and resid 618 through 620 removed outlier: 4.000A pdb=" N VAL K 620 " --> pdb=" O LEU K 659 " (cutoff:3.500A) Processing sheet with id= KE, first strand: chain 'K' and resid 623 through 624 removed outlier: 3.659A pdb=" N GLU K 623 " --> pdb=" O SER K 684 " (cutoff:3.500A) Processing sheet with id= KF, first strand: chain 'K' and resid 693 through 696 removed outlier: 7.296A pdb=" N ARG K 979 " --> pdb=" O ARG K 693 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR K 695 " --> pdb=" O ARG K 979 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N MET K 981 " --> pdb=" O THR K 695 " (cutoff:3.500A) No H-bonds generated for sheet with id= KF Processing sheet with id= KG, first strand: chain 'K' and resid 1009 through 1015 removed outlier: 5.630A pdb=" N VAL K1010 " --> pdb=" O VAL K1027 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K1027 " --> pdb=" O VAL K1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN K1012 " --> pdb=" O LYS K1025 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU K 980 " --> pdb=" O ILE K1059 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE K1059 " --> pdb=" O LEU K 980 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA K 982 " --> pdb=" O TRP K1057 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP K1057 " --> pdb=" O ALA K 982 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET K 984 " --> pdb=" O SER K1055 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER K1055 " --> pdb=" O MET K 984 " (cutoff:3.500A) Processing sheet with id= KH, first strand: chain 'K' and resid 1009 through 1015 removed outlier: 5.630A pdb=" N VAL K1010 " --> pdb=" O VAL K1027 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K1027 " --> pdb=" O VAL K1010 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN K1012 " --> pdb=" O LYS K1025 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG K 693 " --> pdb=" O ARG K 979 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR K 695 " --> pdb=" O MET K 981 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N ALA K 983 " --> pdb=" O THR K 695 " (cutoff:3.500A) Processing sheet with id= KI, first strand: chain 'K' and resid 1052 through 1059 removed outlier: 6.569A pdb=" N LEU K1052 " --> pdb=" O ASP K 988 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP K 988 " --> pdb=" O LEU K1052 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE K1054 " --> pdb=" O THR K 986 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR K 986 " --> pdb=" O PHE K1054 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS K1056 " --> pdb=" O MET K 984 " (cutoff:3.500A) Processing sheet with id= KJ, first strand: chain 'K' and resid 750 through 757 removed outlier: 7.462A pdb=" N THR K 750 " --> pdb=" O TRP K 897 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TRP K 897 " --> pdb=" O THR K 750 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER K 752 " --> pdb=" O GLU K 895 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K 756 " --> pdb=" O CYS K 891 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS K 891 " --> pdb=" O MET K 756 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 787 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 321 basepair parallelities 519 stacking parallelities Total time for adding SS restraints: 48.04 Time building geometry restraints manager: 25.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5625 1.32 - 1.45: 19879 1.45 - 1.58: 22157 1.58 - 1.70: 2273 1.70 - 1.83: 200 Bond restraints: 50134 Sorted by residual: bond pdb=" CG ASP A 295 " pdb=" OD1 ASP A 295 " ideal model delta sigma weight residual 1.249 1.337 -0.088 1.90e-02 2.77e+03 2.14e+01 bond pdb=" CA PRO A 82 " pdb=" C PRO A 82 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.72e+01 bond pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.28e-02 6.10e+03 1.65e+01 bond pdb=" O3' A N2405 " pdb=" P A N2406 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.64e+01 bond pdb=" O3' U N1550 " pdb=" P A N1551 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.64e+01 ... (remaining 50129 not shown) Histogram of bond angle deviations from ideal: 96.90 - 105.39: 5832 105.39 - 113.87: 30093 113.87 - 122.35: 25665 122.35 - 130.84: 11327 130.84 - 139.32: 430 Bond angle restraints: 73347 Sorted by residual: angle pdb=" O3' A N3477 " pdb=" C3' A N3477 " pdb=" C2' A N3477 " ideal model delta sigma weight residual 113.70 96.90 16.80 1.50e+00 4.44e-01 1.25e+02 angle pdb=" O3' C N2625 " pdb=" C3' C N2625 " pdb=" C2' C N2625 " ideal model delta sigma weight residual 109.50 125.10 -15.60 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C4' G N3231 " pdb=" C3' G N3231 " pdb=" O3' G N3231 " ideal model delta sigma weight residual 113.00 98.82 14.18 1.50e+00 4.44e-01 8.94e+01 angle pdb=" O3' U N1550 " pdb=" C3' U N1550 " pdb=" C2' U N1550 " ideal model delta sigma weight residual 109.50 123.46 -13.96 1.50e+00 4.44e-01 8.66e+01 angle pdb=" C HIS A 259 " pdb=" N PRO A 260 " pdb=" CA PRO A 260 " ideal model delta sigma weight residual 121.00 111.79 9.21 1.16e+00 7.43e-01 6.31e+01 ... (remaining 73342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 28305 35.66 - 71.32: 2983 71.32 - 106.98: 328 106.98 - 142.64: 14 142.64 - 178.30: 41 Dihedral angle restraints: 31671 sinusoidal: 23596 harmonic: 8075 Sorted by residual: dihedral pdb=" C5' C N2625 " pdb=" C4' C N2625 " pdb=" C3' C N2625 " pdb=" O3' C N2625 " ideal model delta sinusoidal sigma weight residual 147.00 69.66 77.34 1 8.00e+00 1.56e-02 1.17e+02 dihedral pdb=" C5' C N3328 " pdb=" C4' C N3328 " pdb=" C3' C N3328 " pdb=" O3' C N3328 " ideal model delta sinusoidal sigma weight residual 147.00 70.14 76.86 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C4' C N3328 " pdb=" C3' C N3328 " pdb=" C2' C N3328 " pdb=" C1' C N3328 " ideal model delta sinusoidal sigma weight residual -35.00 34.86 -69.86 1 8.00e+00 1.56e-02 9.83e+01 ... (remaining 31668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.226: 8809 0.226 - 0.453: 371 0.453 - 0.679: 5 0.679 - 0.905: 0 0.905 - 1.132: 1 Chirality restraints: 9186 Sorted by residual: chirality pdb=" C4' A N1221 " pdb=" C5' A N1221 " pdb=" O4' A N1221 " pdb=" C3' A N1221 " both_signs ideal model delta sigma weight residual False -2.50 -1.36 -1.13 2.00e-01 2.50e+01 3.20e+01 chirality pdb=" C3' C N3328 " pdb=" C4' C N3328 " pdb=" O3' C N3328 " pdb=" C2' C N3328 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" C3' U N1550 " pdb=" C4' U N1550 " pdb=" O3' U N1550 " pdb=" C2' U N1550 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.31e+00 ... (remaining 9183 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N3379 " 0.003 2.00e-02 2.50e+03 5.85e-02 7.70e+01 pdb=" N1 C N3379 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C N3379 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C N3379 " -0.071 2.00e-02 2.50e+03 pdb=" N3 C N3379 " 0.144 2.00e-02 2.50e+03 pdb=" C4 C N3379 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C N3379 " -0.070 2.00e-02 2.50e+03 pdb=" C5 C N3379 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C N3379 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3349 " -0.018 2.00e-02 2.50e+03 4.24e-02 4.05e+01 pdb=" N1 C N3349 " 0.013 2.00e-02 2.50e+03 pdb=" C2 C N3349 " -0.008 2.00e-02 2.50e+03 pdb=" O2 C N3349 " 0.062 2.00e-02 2.50e+03 pdb=" N3 C N3349 " -0.101 2.00e-02 2.50e+03 pdb=" C4 C N3349 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C N3349 " 0.038 2.00e-02 2.50e+03 pdb=" C5 C N3349 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C N3349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N1598 " -0.060 2.00e-02 2.50e+03 4.08e-02 3.74e+01 pdb=" N1 U N1598 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U N1598 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U N1598 " -0.009 2.00e-02 2.50e+03 pdb=" N3 U N1598 " 0.060 2.00e-02 2.50e+03 pdb=" C4 U N1598 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U N1598 " -0.074 2.00e-02 2.50e+03 pdb=" C5 U N1598 " 0.023 2.00e-02 2.50e+03 pdb=" C6 U N1598 " 0.014 2.00e-02 2.50e+03 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.70: 2790 2.70 - 3.43: 63348 3.43 - 4.17: 140159 4.17 - 4.90: 201938 Nonbonded interactions: 408237 Sorted by model distance: nonbonded pdb=" N1 A N2425 " pdb=" O4 U N2442 " model vdw 1.236 2.496 nonbonded pdb=" C2 A N2425 " pdb=" O4 U N2442 " model vdw 1.928 3.340 nonbonded pdb=" OH TYR E 92 " pdb=" O2 C N3386 " model vdw 2.014 2.440 nonbonded pdb=" O2' U N3287 " pdb=" OP2 U N3288 " model vdw 2.116 2.440 nonbonded pdb=" O ALA B 66 " pdb=" O2' A N3449 " model vdw 2.164 2.440 ... (remaining 408232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.520 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: 0.040 Extract box with map and model: 8.430 Check model and map are aligned: 0.640 Set scattering table: 0.410 Process input model: 162.360 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.008 0.088 50134 Z= 0.510 Angle : 1.355 16.797 73347 Z= 0.902 Chirality : 0.103 1.132 9186 Planarity : 0.007 0.075 5036 Dihedral : 23.789 178.303 26452 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 3.63 % Allowed : 13.63 % Favored : 82.74 % Rotamer: Outliers : 4.21 % Allowed : 9.42 % Favored : 86.36 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.33 (0.12), residues: 2781 helix: -0.87 (0.17), residues: 618 sheet: -3.37 (0.26), residues: 237 loop : -3.81 (0.11), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP K 824 HIS 0.012 0.003 HIS E 84 PHE 0.043 0.003 PHE A 229 TYR 0.040 0.003 TYR A 275 ARG 0.010 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 590 time to evaluate : 3.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 PRO cc_start: 0.6565 (Cg_endo) cc_final: 0.5867 (Cg_exo) REVERT: A 35 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: A 62 LYS cc_start: 0.7857 (tttt) cc_final: 0.7290 (ttpt) REVERT: A 97 GLN cc_start: 0.5759 (OUTLIER) cc_final: 0.4958 (mp10) REVERT: A 100 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4763 (tptp) REVERT: A 113 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7971 (p0) REVERT: A 121 ASN cc_start: 0.5098 (OUTLIER) cc_final: 0.4725 (m-40) REVERT: A 135 VAL cc_start: 0.5432 (OUTLIER) cc_final: 0.5121 (m) REVERT: A 154 ILE cc_start: 0.8736 (pt) cc_final: 0.8433 (mt) REVERT: A 155 LYS cc_start: 0.6911 (tttt) cc_final: 0.6634 (ttpt) REVERT: A 170 HIS cc_start: 0.6371 (m90) cc_final: 0.6091 (m-70) REVERT: A 180 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6833 (m170) REVERT: A 201 ASN cc_start: 0.8195 (m-40) cc_final: 0.7886 (m-40) REVERT: A 230 ASN cc_start: 0.9132 (p0) cc_final: 0.8858 (p0) REVERT: A 235 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8249 (ttt180) REVERT: A 269 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8635 (tpt-90) REVERT: A 319 PHE cc_start: 0.7401 (m-80) cc_final: 0.6656 (m-10) REVERT: A 332 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 335 CYS cc_start: 0.8214 (m) cc_final: 0.8010 (p) REVERT: A 347 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5777 (mtm110) REVERT: A 348 LYS cc_start: 0.8753 (mttm) cc_final: 0.8327 (tttt) REVERT: A 349 SER cc_start: 0.8883 (m) cc_final: 0.8653 (m) REVERT: A 366 PHE cc_start: 0.5858 (m-80) cc_final: 0.5224 (m-80) REVERT: B 51 LYS cc_start: 0.8014 (pttm) cc_final: 0.7606 (mmmm) REVERT: B 67 CYS cc_start: 0.8516 (m) cc_final: 0.7766 (t) REVERT: B 69 LYS cc_start: 0.8042 (tttt) cc_final: 0.7655 (tptm) REVERT: B 71 ILE cc_start: 0.8384 (mt) cc_final: 0.8005 (mt) REVERT: B 90 MET cc_start: 0.6814 (mtp) cc_final: 0.5934 (mtm) REVERT: B 97 PHE cc_start: 0.6662 (m-80) cc_final: 0.6417 (m-80) REVERT: B 99 ILE cc_start: 0.8951 (tt) cc_final: 0.8705 (mt) REVERT: B 105 ASP cc_start: 0.7181 (m-30) cc_final: 0.6938 (p0) REVERT: B 126 LEU cc_start: 0.9393 (mt) cc_final: 0.9102 (mp) REVERT: B 155 SER cc_start: 0.9018 (m) cc_final: 0.8557 (p) REVERT: B 179 VAL cc_start: 0.9091 (t) cc_final: 0.8738 (t) REVERT: C 15 LYS cc_start: 0.4562 (tttm) cc_final: 0.3542 (mttt) REVERT: C 32 ASP cc_start: 0.3037 (OUTLIER) cc_final: 0.2101 (t0) REVERT: C 159 ILE cc_start: 0.5472 (pt) cc_final: 0.5212 (tt) REVERT: D 21 GLU cc_start: 0.3698 (pt0) cc_final: 0.3390 (pm20) REVERT: E 48 ARG cc_start: 0.7091 (ttm-80) cc_final: 0.6679 (ttt90) REVERT: E 81 GLN cc_start: 0.8622 (mp10) cc_final: 0.7909 (mp10) REVERT: E 94 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.5231 (t80) REVERT: F 9 TYR cc_start: 0.8561 (m-80) cc_final: 0.8186 (m-10) REVERT: F 10 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.5105 (tmt90) REVERT: F 18 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8232 (pt) REVERT: F 39 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8502 (mtmm) REVERT: F 99 ILE cc_start: 0.7615 (mt) cc_final: 0.7355 (mt) REVERT: F 115 MET cc_start: 0.8169 (ttt) cc_final: 0.7687 (ttt) REVERT: F 125 THR cc_start: 0.8540 (m) cc_final: 0.8171 (p) REVERT: F 126 VAL cc_start: 0.9083 (p) cc_final: 0.8698 (m) REVERT: F 154 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7575 (mpt180) REVERT: F 179 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.4044 (pp20) REVERT: F 181 TYR cc_start: 0.7645 (t80) cc_final: 0.7385 (t80) REVERT: F 197 VAL cc_start: 0.8466 (m) cc_final: 0.8042 (t) REVERT: G 1 MET cc_start: 0.5604 (mmm) cc_final: 0.4736 (tpp) REVERT: G 25 ASP cc_start: 0.7696 (p0) cc_final: 0.7114 (p0) REVERT: H 26 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mp) REVERT: H 42 ASN cc_start: 0.6852 (m110) cc_final: 0.6459 (m-40) REVERT: J 45 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5592 (mptt) REVERT: J 58 VAL cc_start: 0.8841 (m) cc_final: 0.8485 (t) REVERT: J 67 LYS cc_start: 0.8273 (mttt) cc_final: 0.7826 (mttm) REVERT: K 9 MET cc_start: -0.0526 (mtt) cc_final: -0.0808 (mtt) REVERT: K 252 TYR cc_start: 0.4229 (OUTLIER) cc_final: 0.3703 (m-80) REVERT: K 264 MET cc_start: 0.6041 (mtm) cc_final: 0.5616 (ttp) REVERT: K 337 PRO cc_start: 0.7094 (Cg_endo) cc_final: 0.6869 (Cg_exo) REVERT: K 349 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4376 (mt) REVERT: K 358 MET cc_start: 0.0574 (mmt) cc_final: 0.0182 (mmt) REVERT: K 373 ARG cc_start: 0.2411 (ptt180) cc_final: 0.1878 (ptt180) REVERT: K 378 MET cc_start: 0.1297 (mtp) cc_final: 0.0917 (mmm) REVERT: K 431 ARG cc_start: 0.2960 (OUTLIER) cc_final: 0.1529 (ptp-110) REVERT: K 530 SER cc_start: 0.4402 (m) cc_final: 0.4074 (p) REVERT: K 536 ARG cc_start: 0.1028 (ptp-170) cc_final: 0.0662 (ptp90) REVERT: K 555 MET cc_start: 0.1843 (mmt) cc_final: 0.1522 (mmt) REVERT: K 630 MET cc_start: 0.4727 (mtt) cc_final: 0.4110 (mtp) REVERT: K 721 MET cc_start: -0.0764 (OUTLIER) cc_final: -0.1787 (pmm) REVERT: K 838 ASN cc_start: 0.5757 (m110) cc_final: 0.5556 (p0) REVERT: K 849 THR cc_start: 0.3838 (m) cc_final: 0.3468 (m) REVERT: K 862 TYR cc_start: 0.0359 (m-80) cc_final: 0.0018 (m-80) REVERT: K 965 MET cc_start: 0.5330 (mtt) cc_final: 0.5100 (mmt) REVERT: K 1015 MET cc_start: 0.1984 (mtt) cc_final: -0.0900 (tpt) REVERT: K 1021 MET cc_start: 0.2775 (mmt) cc_final: 0.2216 (ptm) REVERT: K 1039 GLU cc_start: 0.2450 (tp30) cc_final: 0.2122 (tm-30) REVERT: K 1091 MET cc_start: 0.3203 (ptp) cc_final: 0.2332 (ptp) outliers start: 102 outliers final: 33 residues processed: 667 average time/residue: 0.7055 time to fit residues: 753.8586 Evaluate side-chains 440 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 387 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 306 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 355 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 108 GLN A 166 HIS A 170 HIS A 180 HIS ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 215 ASN A 277 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS C 93 ASN D 152 GLN ** E 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 47 ASN E 98 ASN F 59 GLN F 73 ASN F 143 ASN F 177 ASN F 217 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN J 52 GLN J 147 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 138 ASN K 172 GLN K 247 HIS K 295 GLN K 459 GLN K 641 ASN K 793 HIS K 809 GLN K 844 GLN K 925 ASN K 931 GLN ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 50134 Z= 0.226 Angle : 0.780 11.346 73347 Z= 0.401 Chirality : 0.044 0.282 9186 Planarity : 0.006 0.074 5036 Dihedral : 23.880 179.596 20801 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.22 % Allowed : 10.82 % Favored : 87.95 % Rotamer: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.57 (0.14), residues: 2781 helix: 0.24 (0.22), residues: 633 sheet: -3.05 (0.24), residues: 316 loop : -3.47 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP F 171 HIS 0.010 0.002 HIS K1056 PHE 0.027 0.002 PHE A 202 TYR 0.029 0.002 TYR B 94 ARG 0.013 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 2.606 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: A 9 PRO cc_start: 0.6340 (Cg_endo) cc_final: 0.5978 (Cg_exo) REVERT: A 106 TRP cc_start: 0.7378 (m-90) cc_final: 0.7058 (m-90) REVERT: A 154 ILE cc_start: 0.8537 (pt) cc_final: 0.8289 (mt) REVERT: A 230 ASN cc_start: 0.8825 (p0) cc_final: 0.8248 (p0) REVERT: A 329 PHE cc_start: 0.7504 (p90) cc_final: 0.7235 (p90) REVERT: A 340 ARG cc_start: 0.6398 (mtt180) cc_final: 0.6003 (mtt90) REVERT: A 348 LYS cc_start: 0.8408 (mttm) cc_final: 0.7854 (mtpt) REVERT: B 69 LYS cc_start: 0.7973 (tttt) cc_final: 0.7668 (tppp) REVERT: B 88 TYR cc_start: 0.7921 (m-10) cc_final: 0.7713 (m-10) REVERT: B 105 ASP cc_start: 0.6190 (m-30) cc_final: 0.5909 (p0) REVERT: B 126 LEU cc_start: 0.9433 (mt) cc_final: 0.9030 (mp) REVERT: B 155 SER cc_start: 0.9004 (m) cc_final: 0.8709 (p) REVERT: C 15 LYS cc_start: 0.4429 (tttm) cc_final: 0.3774 (mttt) REVERT: C 159 ILE cc_start: 0.5561 (pt) cc_final: 0.5320 (mt) REVERT: D 1 MET cc_start: 0.6691 (mtm) cc_final: 0.6430 (ptp) REVERT: D 111 LYS cc_start: 0.2461 (tttm) cc_final: 0.2225 (mtpt) REVERT: E 59 MET cc_start: 0.7682 (mmm) cc_final: 0.7356 (mmm) REVERT: F 19 LYS cc_start: 0.6234 (mttm) cc_final: 0.5678 (mttm) REVERT: F 39 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8451 (mtmm) REVERT: F 125 THR cc_start: 0.8385 (m) cc_final: 0.8072 (p) REVERT: F 154 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7627 (mtp85) REVERT: F 157 TYR cc_start: 0.7832 (m-80) cc_final: 0.7399 (m-10) REVERT: F 171 TRP cc_start: 0.6809 (m-10) cc_final: 0.6606 (m-10) REVERT: F 191 MET cc_start: 0.6252 (mtm) cc_final: 0.5660 (mtm) REVERT: G 1 MET cc_start: 0.4387 (mmm) cc_final: 0.3631 (mtp) REVERT: G 19 MET cc_start: 0.6579 (tpp) cc_final: 0.6266 (tpp) REVERT: H 20 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7668 (mtt-85) REVERT: J 1 MET cc_start: 0.3960 (mmp) cc_final: 0.3685 (mmt) REVERT: J 21 LYS cc_start: 0.6785 (mtmt) cc_final: 0.5966 (ptpp) REVERT: J 45 LYS cc_start: 0.6064 (mtpt) cc_final: 0.5540 (mttp) REVERT: J 67 LYS cc_start: 0.7297 (mttt) cc_final: 0.7039 (mttm) REVERT: J 164 LYS cc_start: 0.8283 (ttmm) cc_final: 0.8077 (ttpp) REVERT: K 189 ARG cc_start: 0.5027 (mtm180) cc_final: 0.4705 (tpp-160) REVERT: K 221 SER cc_start: 0.3867 (m) cc_final: 0.3628 (p) REVERT: K 264 MET cc_start: 0.5869 (mtm) cc_final: 0.5486 (tmm) REVERT: K 358 MET cc_start: 0.0953 (mmt) cc_final: 0.0569 (mmt) REVERT: K 378 MET cc_start: 0.1385 (mtp) cc_final: 0.1010 (mmm) REVERT: K 431 ARG cc_start: 0.2260 (pmt-80) cc_final: 0.1306 (ptp-110) REVERT: K 536 ARG cc_start: 0.1157 (ptp-170) cc_final: 0.0793 (ptp90) REVERT: K 555 MET cc_start: 0.1919 (mmt) cc_final: 0.1598 (mmt) REVERT: K 564 TYR cc_start: 0.1397 (p90) cc_final: 0.0593 (p90) REVERT: K 630 MET cc_start: 0.4461 (mtt) cc_final: 0.3975 (mmm) REVERT: K 705 VAL cc_start: 0.3157 (m) cc_final: 0.2827 (p) REVERT: K 791 MET cc_start: 0.0052 (mmp) cc_final: -0.1221 (ttt) REVERT: K 981 MET cc_start: 0.4360 (ttm) cc_final: 0.3904 (ttt) REVERT: K 1015 MET cc_start: 0.2208 (mtt) cc_final: -0.1291 (tpt) REVERT: K 1021 MET cc_start: 0.2229 (mmt) cc_final: 0.1548 (ptm) REVERT: K 1039 GLU cc_start: 0.3015 (tp30) cc_final: 0.2564 (tm-30) outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.6302 time to fit residues: 500.6960 Evaluate side-chains 368 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 241 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 137 HIS E 10 ASN F 51 HIS F 217 ASN G 33 ASN G 61 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 171 HIS K 4 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 810 HIS K 818 ASN K 931 GLN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 50134 Z= 0.437 Angle : 1.011 12.725 73347 Z= 0.507 Chirality : 0.052 0.320 9186 Planarity : 0.007 0.101 5036 Dihedral : 24.000 179.996 20801 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 1.19 % Allowed : 14.67 % Favored : 84.14 % Rotamer: Outliers : 0.21 % Allowed : 6.32 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.94 (0.14), residues: 2781 helix: -0.76 (0.20), residues: 630 sheet: -3.03 (0.27), residues: 247 loop : -3.48 (0.12), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP G 51 HIS 0.011 0.003 HIS A 276 PHE 0.033 0.004 PHE A 373 TYR 0.030 0.003 TYR F 17 ARG 0.027 0.001 ARG K 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 420 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8024 (m-30) cc_final: 0.7779 (m-30) REVERT: A 106 TRP cc_start: 0.7411 (m-90) cc_final: 0.6987 (m-90) REVERT: A 155 LYS cc_start: 0.7765 (tttt) cc_final: 0.7548 (mtmm) REVERT: A 192 VAL cc_start: 0.9006 (t) cc_final: 0.8731 (p) REVERT: A 235 ARG cc_start: 0.9163 (ttt180) cc_final: 0.8346 (ttt180) REVERT: A 331 MET cc_start: 0.7361 (tpt) cc_final: 0.6944 (tpt) REVERT: A 348 LYS cc_start: 0.8502 (mttm) cc_final: 0.8071 (mtpt) REVERT: B 15 ASN cc_start: 0.7974 (p0) cc_final: 0.7749 (p0) REVERT: B 19 ASP cc_start: 0.7488 (t0) cc_final: 0.7100 (t0) REVERT: B 62 ARG cc_start: 0.5734 (mmm-85) cc_final: 0.5502 (mmt180) REVERT: B 69 LYS cc_start: 0.8199 (tttt) cc_final: 0.7861 (tptm) REVERT: B 126 LEU cc_start: 0.9422 (mt) cc_final: 0.9056 (mp) REVERT: B 155 SER cc_start: 0.9045 (m) cc_final: 0.8779 (p) REVERT: C 19 LEU cc_start: 0.8565 (tp) cc_final: 0.8291 (tp) REVERT: G 1 MET cc_start: 0.4734 (mmm) cc_final: 0.4264 (mtp) REVERT: H 20 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7783 (mtt-85) REVERT: J 1 MET cc_start: 0.4432 (mmp) cc_final: 0.4210 (mmt) REVERT: J 21 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6034 (ptpp) REVERT: J 45 LYS cc_start: 0.6534 (mtpt) cc_final: 0.6052 (mptt) REVERT: J 50 VAL cc_start: 0.8798 (m) cc_final: 0.8510 (p) REVERT: J 51 LEU cc_start: 0.8095 (mp) cc_final: 0.7731 (pp) REVERT: J 67 LYS cc_start: 0.7989 (mttt) cc_final: 0.7437 (mttm) REVERT: K 1 MET cc_start: 0.3510 (ptt) cc_final: 0.3136 (mmt) REVERT: K 57 MET cc_start: -0.1759 (ttp) cc_final: -0.1998 (ttm) REVERT: K 264 MET cc_start: 0.5956 (mtm) cc_final: 0.5648 (tmm) REVERT: K 358 MET cc_start: 0.1175 (mmt) cc_final: 0.0935 (mmt) REVERT: K 378 MET cc_start: 0.0852 (mtp) cc_final: 0.0596 (mtt) REVERT: K 393 GLN cc_start: 0.5332 (tp40) cc_final: 0.4971 (tp40) REVERT: K 447 GLN cc_start: 0.1938 (pt0) cc_final: 0.1414 (tp40) REVERT: K 499 GLU cc_start: 0.2770 (mt-10) cc_final: 0.1882 (pm20) REVERT: K 555 MET cc_start: 0.2844 (mmt) cc_final: 0.2513 (mmt) REVERT: K 564 TYR cc_start: 0.0695 (p90) cc_final: 0.0190 (p90) REVERT: K 630 MET cc_start: 0.4285 (mtt) cc_final: 0.3943 (mmm) REVERT: K 776 MET cc_start: 0.3961 (tpp) cc_final: 0.3327 (tpp) REVERT: K 791 MET cc_start: -0.0006 (mmp) cc_final: -0.0559 (mpp) REVERT: K 888 MET cc_start: 0.3535 (tmm) cc_final: 0.2707 (tpp) REVERT: K 984 MET cc_start: 0.1145 (mmm) cc_final: 0.0931 (mmm) REVERT: K 1006 ARG cc_start: 0.6054 (mpp80) cc_final: 0.5645 (ptp-110) REVERT: K 1015 MET cc_start: 0.2754 (mtt) cc_final: -0.1225 (tpt) REVERT: K 1021 MET cc_start: 0.2122 (mmt) cc_final: 0.1393 (ptt) REVERT: K 1091 MET cc_start: 0.3770 (mpp) cc_final: 0.2462 (mpp) outliers start: 5 outliers final: 2 residues processed: 425 average time/residue: 0.6253 time to fit residues: 430.2257 Evaluate side-chains 338 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 336 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN D 152 GLN E 10 ASN F 51 HIS F 177 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 171 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 254 GLN K 435 GLN K 466 GLN K 844 GLN ** K1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 50134 Z= 0.310 Angle : 0.832 10.297 73347 Z= 0.421 Chirality : 0.045 0.291 9186 Planarity : 0.006 0.086 5036 Dihedral : 23.805 179.893 20801 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 1.15 % Allowed : 12.19 % Favored : 86.66 % Rotamer: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.94 (0.14), residues: 2781 helix: -0.83 (0.20), residues: 631 sheet: -2.85 (0.27), residues: 264 loop : -3.48 (0.12), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 171 HIS 0.012 0.002 HIS A 277 PHE 0.056 0.003 PHE B 116 TYR 0.036 0.003 TYR F 17 ARG 0.005 0.001 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 412 time to evaluate : 3.537 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: A 106 TRP cc_start: 0.7290 (m-90) cc_final: 0.6900 (m-90) REVERT: A 190 SER cc_start: 0.7650 (p) cc_final: 0.7404 (p) REVERT: A 235 ARG cc_start: 0.9029 (ttt180) cc_final: 0.8318 (ttt180) REVERT: B 19 ASP cc_start: 0.7518 (t0) cc_final: 0.7125 (t0) REVERT: B 69 LYS cc_start: 0.8141 (tttt) cc_final: 0.7698 (tptm) REVERT: B 126 LEU cc_start: 0.9398 (mt) cc_final: 0.9152 (mp) REVERT: B 154 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: B 179 VAL cc_start: 0.8551 (t) cc_final: 0.8250 (p) REVERT: C 15 LYS cc_start: 0.5701 (tttm) cc_final: 0.5232 (mttt) REVERT: C 44 LYS cc_start: 0.5905 (mtpp) cc_final: 0.5474 (tptt) REVERT: E 135 ILE cc_start: 0.7697 (mm) cc_final: 0.7249 (mp) REVERT: F 19 LYS cc_start: 0.6292 (mttt) cc_final: 0.6079 (mttt) REVERT: H 14 CYS cc_start: 0.6836 (m) cc_final: 0.6634 (m) REVERT: J 1 MET cc_start: 0.4858 (mmp) cc_final: 0.4596 (mmt) REVERT: J 21 LYS cc_start: 0.6726 (mtmt) cc_final: 0.5762 (ptpp) REVERT: J 45 LYS cc_start: 0.6969 (mtpt) cc_final: 0.6266 (mptt) REVERT: J 50 VAL cc_start: 0.8769 (m) cc_final: 0.8450 (p) REVERT: J 51 LEU cc_start: 0.7928 (mp) cc_final: 0.7622 (pp) REVERT: J 67 LYS cc_start: 0.7846 (mttt) cc_final: 0.7354 (mttm) REVERT: K 30 HIS cc_start: 0.4030 (t70) cc_final: 0.3743 (t-170) REVERT: K 91 ILE cc_start: 0.1454 (OUTLIER) cc_final: -0.0071 (pt) REVERT: K 264 MET cc_start: 0.5995 (mtm) cc_final: 0.5579 (tmm) REVERT: K 358 MET cc_start: 0.1136 (mmt) cc_final: 0.0759 (mmt) REVERT: K 393 GLN cc_start: 0.5216 (tp40) cc_final: 0.4781 (tp40) REVERT: K 444 ARG cc_start: 0.5048 (mmp80) cc_final: 0.4001 (mmp-170) REVERT: K 447 GLN cc_start: 0.2541 (pt0) cc_final: 0.1969 (tp40) REVERT: K 564 TYR cc_start: 0.0607 (p90) cc_final: 0.0119 (p90) REVERT: K 756 MET cc_start: 0.0281 (ttp) cc_final: -0.0034 (ttp) REVERT: K 776 MET cc_start: 0.3480 (tpp) cc_final: 0.2698 (tpp) REVERT: K 791 MET cc_start: 0.0307 (mmp) cc_final: -0.0192 (mpp) REVERT: K 806 LYS cc_start: 0.5113 (mttt) cc_final: 0.4890 (mtmm) REVERT: K 987 CYS cc_start: 0.7140 (m) cc_final: 0.6276 (p) REVERT: K 1006 ARG cc_start: 0.5801 (mpp80) cc_final: 0.5204 (ptp-110) REVERT: K 1015 MET cc_start: 0.2380 (mtt) cc_final: -0.1603 (tpt) REVERT: K 1021 MET cc_start: 0.1979 (mmt) cc_final: 0.1228 (ptt) REVERT: K 1091 MET cc_start: 0.2510 (mpp) cc_final: 0.1683 (mpp) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.6370 time to fit residues: 428.0225 Evaluate side-chains 332 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 330 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 339 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS E 10 ASN F 177 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 HIS ** K1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 50134 Z= 0.220 Angle : 0.732 12.169 73347 Z= 0.372 Chirality : 0.041 0.300 9186 Planarity : 0.005 0.080 5036 Dihedral : 23.580 179.113 20801 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 1.04 % Allowed : 12.33 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.72 (0.14), residues: 2781 helix: -0.59 (0.20), residues: 620 sheet: -2.66 (0.25), residues: 304 loop : -3.35 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 171 HIS 0.008 0.002 HIS A 277 PHE 0.053 0.002 PHE B 116 TYR 0.037 0.002 TYR F 181 ARG 0.005 0.001 ARG K 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7128 (tpp) cc_final: 0.6679 (mtp) REVERT: A 59 ASP cc_start: 0.8086 (m-30) cc_final: 0.7707 (m-30) REVERT: A 235 ARG cc_start: 0.8957 (ttt180) cc_final: 0.8280 (ttt180) REVERT: B 30 PRO cc_start: 0.7396 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: B 62 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6500 (mmm160) REVERT: B 69 LYS cc_start: 0.8194 (tttt) cc_final: 0.7741 (tptm) REVERT: B 126 LEU cc_start: 0.9362 (mt) cc_final: 0.9029 (mp) REVERT: C 19 LEU cc_start: 0.8621 (tp) cc_final: 0.8338 (tp) REVERT: C 44 LYS cc_start: 0.5826 (mtpp) cc_final: 0.5452 (tptt) REVERT: E 35 TYR cc_start: 0.8202 (t80) cc_final: 0.7973 (t80) REVERT: E 56 ASP cc_start: 0.7774 (p0) cc_final: 0.7481 (p0) REVERT: E 88 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7596 (mmtt) REVERT: E 135 ILE cc_start: 0.8050 (mm) cc_final: 0.7744 (mp) REVERT: F 200 ILE cc_start: 0.8685 (mt) cc_final: 0.8440 (mt) REVERT: H 14 CYS cc_start: 0.6901 (m) cc_final: 0.6681 (m) REVERT: J 1 MET cc_start: 0.4705 (mmp) cc_final: 0.4439 (mmt) REVERT: J 21 LYS cc_start: 0.6508 (mtmt) cc_final: 0.5747 (ptpp) REVERT: J 45 LYS cc_start: 0.6298 (mtpt) cc_final: 0.5709 (mptt) REVERT: J 50 VAL cc_start: 0.8606 (m) cc_final: 0.8305 (p) REVERT: J 54 HIS cc_start: 0.6868 (t70) cc_final: 0.6439 (t-90) REVERT: J 67 LYS cc_start: 0.7747 (mttt) cc_final: 0.7333 (mttm) REVERT: J 103 GLN cc_start: 0.6125 (mm-40) cc_final: 0.5415 (mm-40) REVERT: K 264 MET cc_start: 0.5989 (mtm) cc_final: 0.5551 (tmm) REVERT: K 358 MET cc_start: 0.1251 (mmt) cc_final: 0.0874 (mmt) REVERT: K 393 GLN cc_start: 0.5114 (tp40) cc_final: 0.4793 (tp40) REVERT: K 447 GLN cc_start: 0.2513 (pt0) cc_final: 0.1881 (tp40) REVERT: K 520 LYS cc_start: 0.1417 (ttpp) cc_final: 0.0265 (tptt) REVERT: K 625 LYS cc_start: 0.4823 (mttt) cc_final: 0.4495 (mtpt) REVERT: K 630 MET cc_start: 0.3669 (mmm) cc_final: 0.3150 (mmm) REVERT: K 791 MET cc_start: 0.1141 (mmp) cc_final: 0.0754 (mpp) REVERT: K 806 LYS cc_start: 0.5407 (mttt) cc_final: 0.5126 (mtmm) REVERT: K 987 CYS cc_start: 0.6604 (m) cc_final: 0.5802 (p) REVERT: K 1006 ARG cc_start: 0.5592 (mpp80) cc_final: 0.5144 (ptp-110) REVERT: K 1015 MET cc_start: 0.1669 (mtt) cc_final: -0.1271 (tpt) REVERT: K 1021 MET cc_start: 0.2245 (mmt) cc_final: 0.1580 (ptt) REVERT: K 1091 MET cc_start: 0.4278 (mpp) cc_final: 0.3829 (mpp) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.6273 time to fit residues: 437.1547 Evaluate side-chains 345 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 93 optimal weight: 0.0370 chunk 378 optimal weight: 10.0000 chunk 314 optimal weight: 10.9990 chunk 175 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS C 155 ASN E 10 ASN F 177 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 254 GLN K 334 HIS K 342 ASN K 554 HIS K 632 GLN ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 50134 Z= 0.307 Angle : 0.819 11.229 73347 Z= 0.413 Chirality : 0.044 0.313 9186 Planarity : 0.006 0.077 5036 Dihedral : 23.648 178.667 20801 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 1.04 % Allowed : 13.63 % Favored : 85.33 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.74 (0.14), residues: 2781 helix: -0.73 (0.20), residues: 619 sheet: -2.54 (0.26), residues: 288 loop : -3.34 (0.12), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 171 HIS 0.010 0.002 HIS A 277 PHE 0.026 0.002 PHE B 116 TYR 0.029 0.003 TYR F 17 ARG 0.007 0.001 ARG J 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7608 (tpp) cc_final: 0.6787 (tpp) REVERT: A 59 ASP cc_start: 0.8004 (m-30) cc_final: 0.7744 (m-30) REVERT: A 157 ARG cc_start: 0.4538 (mtt180) cc_final: 0.4105 (mtm110) REVERT: A 348 LYS cc_start: 0.8450 (mttm) cc_final: 0.7784 (mtpt) REVERT: A 356 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7922 (mtp85) REVERT: B 19 ASP cc_start: 0.7694 (t0) cc_final: 0.7433 (t0) REVERT: B 30 PRO cc_start: 0.7439 (Cg_endo) cc_final: 0.7156 (Cg_exo) REVERT: B 62 ARG cc_start: 0.6724 (mtp180) cc_final: 0.6424 (mmt180) REVERT: B 69 LYS cc_start: 0.8421 (tttt) cc_final: 0.7981 (tptm) REVERT: B 93 VAL cc_start: 0.8195 (p) cc_final: 0.7781 (p) REVERT: B 97 PHE cc_start: 0.5901 (m-80) cc_final: 0.5696 (m-80) REVERT: C 15 LYS cc_start: 0.5743 (tttm) cc_final: 0.5382 (mttp) REVERT: C 19 LEU cc_start: 0.8631 (tp) cc_final: 0.8423 (tp) REVERT: C 33 PHE cc_start: 0.7468 (p90) cc_final: 0.7131 (p90) REVERT: C 44 LYS cc_start: 0.5730 (mtpp) cc_final: 0.5257 (tptt) REVERT: C 59 MET cc_start: 0.7009 (ptm) cc_final: 0.5963 (ttp) REVERT: E 56 ASP cc_start: 0.7858 (p0) cc_final: 0.7570 (p0) REVERT: E 70 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8315 (ttm-80) REVERT: G 1 MET cc_start: 0.5676 (ttt) cc_final: 0.3891 (ttt) REVERT: H 14 CYS cc_start: 0.7123 (m) cc_final: 0.6764 (m) REVERT: J 1 MET cc_start: 0.4965 (mmp) cc_final: 0.4757 (mmt) REVERT: J 21 LYS cc_start: 0.6381 (mtmt) cc_final: 0.5568 (ptpp) REVERT: J 45 LYS cc_start: 0.6592 (mtpt) cc_final: 0.5917 (mptt) REVERT: J 50 VAL cc_start: 0.8335 (m) cc_final: 0.8108 (p) REVERT: J 67 LYS cc_start: 0.7917 (mttt) cc_final: 0.7354 (mttm) REVERT: J 103 GLN cc_start: 0.6012 (mm-40) cc_final: 0.5279 (mm-40) REVERT: K 40 ILE cc_start: 0.6430 (mp) cc_final: 0.6149 (mp) REVERT: K 57 MET cc_start: -0.2314 (ttm) cc_final: -0.3032 (tpt) REVERT: K 264 MET cc_start: 0.5948 (mtm) cc_final: 0.5507 (tmm) REVERT: K 358 MET cc_start: 0.1330 (mmt) cc_final: 0.0959 (mmt) REVERT: K 393 GLN cc_start: 0.5155 (tp40) cc_final: 0.4773 (tp40) REVERT: K 447 GLN cc_start: 0.2594 (pt0) cc_final: 0.2000 (tp40) REVERT: K 520 LYS cc_start: 0.1427 (ttpp) cc_final: 0.0211 (tptt) REVERT: K 625 LYS cc_start: 0.4608 (mttt) cc_final: 0.4298 (mtpt) REVERT: K 630 MET cc_start: 0.3734 (mmm) cc_final: 0.3201 (mmm) REVERT: K 763 THR cc_start: 0.3491 (m) cc_final: 0.3237 (m) REVERT: K 791 MET cc_start: 0.1364 (mmp) cc_final: 0.1067 (mpp) REVERT: K 888 MET cc_start: 0.3682 (tmm) cc_final: 0.3327 (tmm) REVERT: K 987 CYS cc_start: 0.6758 (m) cc_final: 0.6100 (p) REVERT: K 1006 ARG cc_start: 0.5807 (mpp80) cc_final: 0.5320 (ptp-110) REVERT: K 1015 MET cc_start: 0.0774 (mtt) cc_final: -0.1700 (tpt) REVERT: K 1021 MET cc_start: 0.2385 (mmt) cc_final: 0.1795 (ptt) REVERT: K 1091 MET cc_start: 0.4346 (mpp) cc_final: 0.3847 (mpp) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.6313 time to fit residues: 414.9462 Evaluate side-chains 332 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 276 optimal weight: 30.0000 chunk 214 optimal weight: 0.7980 chunk 318 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 376 optimal weight: 9.9990 chunk 235 optimal weight: 0.5980 chunk 229 optimal weight: 5.9990 chunk 173 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 177 ASN G 61 ASN H 32 ASN ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** K 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN K 231 ASN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN K 845 ASN K1109 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 50134 Z= 0.158 Angle : 0.659 10.862 73347 Z= 0.336 Chirality : 0.038 0.330 9186 Planarity : 0.005 0.084 5036 Dihedral : 23.407 179.870 20801 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 1.01 % Allowed : 10.32 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.43 (0.14), residues: 2781 helix: -0.39 (0.21), residues: 618 sheet: -2.45 (0.26), residues: 296 loop : -3.15 (0.12), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP K 135 HIS 0.004 0.001 HIS K 810 PHE 0.019 0.002 PHE B 116 TYR 0.022 0.002 TYR E 92 ARG 0.008 0.001 ARG J 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.303 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: A 47 MET cc_start: 0.7486 (tpp) cc_final: 0.6537 (tpp) REVERT: A 80 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5907 (tm-30) REVERT: A 167 THR cc_start: 0.7863 (t) cc_final: 0.7290 (t) REVERT: A 348 LYS cc_start: 0.8349 (mttm) cc_final: 0.7547 (mtpt) REVERT: A 356 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7935 (mtp85) REVERT: B 12 ILE cc_start: 0.7523 (pt) cc_final: 0.7250 (pt) REVERT: B 30 PRO cc_start: 0.7456 (Cg_endo) cc_final: 0.7177 (Cg_exo) REVERT: B 62 ARG cc_start: 0.6826 (mtp180) cc_final: 0.6341 (mmt180) REVERT: B 69 LYS cc_start: 0.8310 (tttt) cc_final: 0.7899 (tptm) REVERT: C 15 LYS cc_start: 0.5498 (tttm) cc_final: 0.5165 (mttt) REVERT: C 19 LEU cc_start: 0.8599 (tp) cc_final: 0.8370 (tp) REVERT: C 33 PHE cc_start: 0.7442 (p90) cc_final: 0.7149 (p90) REVERT: C 44 LYS cc_start: 0.5887 (mtpp) cc_final: 0.5364 (tptt) REVERT: E 102 MET cc_start: 0.8117 (tpp) cc_final: 0.7824 (tpp) REVERT: F 38 ARG cc_start: 0.7292 (ttm-80) cc_final: 0.7006 (ttm-80) REVERT: G 1 MET cc_start: 0.5111 (ttt) cc_final: 0.3130 (ttt) REVERT: H 14 CYS cc_start: 0.7163 (m) cc_final: 0.6736 (m) REVERT: J 1 MET cc_start: 0.4819 (mmp) cc_final: 0.4604 (mmt) REVERT: J 21 LYS cc_start: 0.5892 (mtmt) cc_final: 0.5347 (ptpp) REVERT: J 67 LYS cc_start: 0.7758 (mttt) cc_final: 0.7133 (mttm) REVERT: J 103 GLN cc_start: 0.6372 (mm-40) cc_final: 0.5609 (mm-40) REVERT: J 194 ILE cc_start: 0.3960 (pt) cc_final: 0.3500 (pt) REVERT: K 40 ILE cc_start: 0.6425 (mp) cc_final: 0.6189 (mp) REVERT: K 57 MET cc_start: -0.2819 (ttm) cc_final: -0.3508 (tpt) REVERT: K 264 MET cc_start: 0.5939 (mtm) cc_final: 0.5525 (tmm) REVERT: K 358 MET cc_start: 0.1271 (mmt) cc_final: 0.0980 (mmt) REVERT: K 393 GLN cc_start: 0.5146 (tp40) cc_final: 0.4828 (tp40) REVERT: K 447 GLN cc_start: 0.2640 (pt0) cc_final: 0.2015 (tp40) REVERT: K 520 LYS cc_start: 0.1507 (ttpp) cc_final: 0.0375 (tptt) REVERT: K 536 ARG cc_start: 0.0396 (ttm170) cc_final: 0.0148 (ttm170) REVERT: K 625 LYS cc_start: 0.4307 (mttt) cc_final: 0.4013 (mtpt) REVERT: K 630 MET cc_start: 0.3832 (mmm) cc_final: 0.3243 (mmm) REVERT: K 791 MET cc_start: 0.0813 (mmp) cc_final: 0.0525 (mpp) REVERT: K 987 CYS cc_start: 0.6898 (m) cc_final: 0.6220 (p) REVERT: K 1006 ARG cc_start: 0.5703 (mpp80) cc_final: 0.5250 (ptp-110) REVERT: K 1015 MET cc_start: 0.0800 (mtt) cc_final: -0.1558 (tpt) REVERT: K 1021 MET cc_start: 0.2712 (mmt) cc_final: 0.2105 (ptm) REVERT: K 1091 MET cc_start: 0.3982 (mpp) cc_final: 0.3297 (mpp) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.6193 time to fit residues: 423.9898 Evaluate side-chains 344 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN D 100 HIS E 10 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 50134 Z= 0.413 Angle : 0.919 10.458 73347 Z= 0.459 Chirality : 0.048 0.349 9186 Planarity : 0.007 0.078 5036 Dihedral : 23.670 179.214 20801 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 1.01 % Allowed : 15.07 % Favored : 83.93 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.72 (0.14), residues: 2781 helix: -0.87 (0.20), residues: 623 sheet: -2.56 (0.26), residues: 292 loop : -3.27 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.005 TRP A 258 HIS 0.013 0.002 HIS A 277 PHE 0.026 0.003 PHE A 388 TYR 0.032 0.003 TYR E 92 ARG 0.008 0.001 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7861 (tpp) cc_final: 0.6760 (tpp) REVERT: A 80 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6195 (tm-30) REVERT: A 304 THR cc_start: 0.6630 (m) cc_final: 0.6328 (t) REVERT: A 348 LYS cc_start: 0.8491 (mttm) cc_final: 0.7842 (mtpt) REVERT: B 11 GLN cc_start: 0.8437 (pp30) cc_final: 0.8184 (pp30) REVERT: B 12 ILE cc_start: 0.8121 (pt) cc_final: 0.7675 (pt) REVERT: B 15 ASN cc_start: 0.7578 (p0) cc_final: 0.7318 (p0) REVERT: B 19 ASP cc_start: 0.7985 (t0) cc_final: 0.7637 (t0) REVERT: B 30 PRO cc_start: 0.7451 (Cg_endo) cc_final: 0.7196 (Cg_exo) REVERT: B 62 ARG cc_start: 0.6707 (mtp180) cc_final: 0.6414 (mmt180) REVERT: B 69 LYS cc_start: 0.8420 (tttt) cc_final: 0.7976 (tptm) REVERT: B 93 VAL cc_start: 0.8337 (p) cc_final: 0.7780 (p) REVERT: C 15 LYS cc_start: 0.5803 (tttm) cc_final: 0.5398 (mttp) REVERT: C 19 LEU cc_start: 0.8580 (tp) cc_final: 0.8327 (tp) REVERT: C 44 LYS cc_start: 0.6873 (mtpp) cc_final: 0.6109 (tptt) REVERT: E 34 LEU cc_start: 0.8420 (mt) cc_final: 0.8049 (mt) REVERT: G 1 MET cc_start: 0.5590 (ttt) cc_final: 0.3816 (ttt) REVERT: H 14 CYS cc_start: 0.7245 (m) cc_final: 0.6853 (m) REVERT: J 21 LYS cc_start: 0.6272 (mtmt) cc_final: 0.5421 (ptpp) REVERT: J 67 LYS cc_start: 0.8066 (mttt) cc_final: 0.7444 (mttm) REVERT: J 103 GLN cc_start: 0.6110 (mm-40) cc_final: 0.5410 (mm-40) REVERT: K 40 ILE cc_start: 0.6620 (mp) cc_final: 0.6350 (mp) REVERT: K 57 MET cc_start: -0.2476 (ttm) cc_final: -0.3054 (tpt) REVERT: K 264 MET cc_start: 0.5807 (mtm) cc_final: 0.5597 (tmm) REVERT: K 270 ASP cc_start: 0.4496 (m-30) cc_final: 0.3951 (p0) REVERT: K 358 MET cc_start: 0.1434 (mmt) cc_final: 0.1107 (mmt) REVERT: K 393 GLN cc_start: 0.5054 (tp40) cc_final: 0.4650 (tp40) REVERT: K 520 LYS cc_start: 0.1600 (ttpp) cc_final: 0.0444 (tptt) REVERT: K 625 LYS cc_start: 0.4083 (mttt) cc_final: 0.3777 (mtpt) REVERT: K 630 MET cc_start: 0.3915 (mmm) cc_final: 0.3185 (mmm) REVERT: K 987 CYS cc_start: 0.6797 (m) cc_final: 0.6108 (p) REVERT: K 1015 MET cc_start: 0.0974 (mtt) cc_final: -0.1582 (tpt) REVERT: K 1091 MET cc_start: 0.4708 (mpp) cc_final: 0.4168 (mpp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.6431 time to fit residues: 405.5009 Evaluate side-chains 320 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 351 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 332 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN F 177 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 50134 Z= 0.329 Angle : 0.853 11.651 73347 Z= 0.431 Chirality : 0.046 0.360 9186 Planarity : 0.006 0.083 5036 Dihedral : 23.733 179.970 20801 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.97 % Allowed : 13.92 % Favored : 85.11 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.77 (0.14), residues: 2781 helix: -0.95 (0.20), residues: 623 sheet: -2.64 (0.26), residues: 294 loop : -3.27 (0.12), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.004 TRP A 258 HIS 0.010 0.002 HIS A 277 PHE 0.023 0.003 PHE B 97 TYR 0.029 0.003 TYR E 92 ARG 0.007 0.001 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7765 (tpp) cc_final: 0.6575 (tpp) REVERT: A 304 THR cc_start: 0.6625 (m) cc_final: 0.6308 (t) REVERT: A 348 LYS cc_start: 0.8468 (mttm) cc_final: 0.7809 (mtpt) REVERT: B 11 GLN cc_start: 0.8433 (pp30) cc_final: 0.8150 (pp30) REVERT: B 12 ILE cc_start: 0.8146 (pt) cc_final: 0.7638 (pt) REVERT: B 19 ASP cc_start: 0.7876 (t0) cc_final: 0.7567 (t0) REVERT: B 62 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6482 (mmt180) REVERT: B 69 LYS cc_start: 0.8446 (tttt) cc_final: 0.7997 (tptm) REVERT: B 93 VAL cc_start: 0.8557 (p) cc_final: 0.8219 (p) REVERT: C 15 LYS cc_start: 0.6016 (tttm) cc_final: 0.5613 (mttp) REVERT: C 19 LEU cc_start: 0.8561 (tp) cc_final: 0.8309 (tp) REVERT: E 56 ASP cc_start: 0.8055 (p0) cc_final: 0.7741 (p0) REVERT: G 1 MET cc_start: 0.5179 (ttt) cc_final: 0.3648 (ttt) REVERT: H 14 CYS cc_start: 0.7490 (m) cc_final: 0.7061 (m) REVERT: J 21 LYS cc_start: 0.5965 (mtmt) cc_final: 0.5665 (ptpp) REVERT: J 67 LYS cc_start: 0.8052 (mttt) cc_final: 0.7400 (mttm) REVERT: J 103 GLN cc_start: 0.6172 (mm-40) cc_final: 0.5466 (mm-40) REVERT: J 169 ARG cc_start: 0.4855 (mtm-85) cc_final: 0.4237 (ptp-110) REVERT: J 194 ILE cc_start: 0.4484 (pt) cc_final: 0.4019 (pt) REVERT: K 40 ILE cc_start: 0.6624 (mp) cc_final: 0.6336 (mp) REVERT: K 57 MET cc_start: -0.2574 (ttm) cc_final: -0.3120 (tpt) REVERT: K 114 ILE cc_start: 0.6243 (pt) cc_final: 0.5928 (mm) REVERT: K 264 MET cc_start: 0.5819 (mtm) cc_final: 0.5583 (tmm) REVERT: K 270 ASP cc_start: 0.4456 (m-30) cc_final: 0.3621 (p0) REVERT: K 358 MET cc_start: 0.1400 (mmt) cc_final: 0.1082 (mmt) REVERT: K 393 GLN cc_start: 0.5014 (tp40) cc_final: 0.4655 (tp40) REVERT: K 520 LYS cc_start: 0.1463 (ttpp) cc_final: 0.0365 (tptt) REVERT: K 630 MET cc_start: 0.3961 (mmm) cc_final: 0.3562 (mmm) REVERT: K 987 CYS cc_start: 0.7011 (m) cc_final: 0.6260 (p) REVERT: K 1015 MET cc_start: 0.0978 (mtt) cc_final: -0.1654 (tpt) REVERT: K 1021 MET cc_start: 0.2294 (mmt) cc_final: 0.1671 (ptt) REVERT: K 1091 MET cc_start: 0.4181 (mpp) cc_final: 0.3131 (mpp) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.6354 time to fit residues: 411.4166 Evaluate side-chains 318 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 239 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN E 10 ASN F 177 ASN J 171 HIS ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 466 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 915 GLN ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1092 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 50134 Z= 0.295 Angle : 0.822 11.231 73347 Z= 0.416 Chirality : 0.044 0.333 9186 Planarity : 0.006 0.075 5036 Dihedral : 23.720 179.909 20801 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.90 % Allowed : 14.96 % Favored : 84.14 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.78 (0.14), residues: 2781 helix: -0.89 (0.20), residues: 627 sheet: -2.69 (0.26), residues: 297 loop : -3.31 (0.12), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP A 258 HIS 0.009 0.002 HIS A 277 PHE 0.023 0.003 PHE B 116 TYR 0.029 0.003 TYR K 573 ARG 0.010 0.001 ARG G 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7733 (tpp) cc_final: 0.7531 (tpp) REVERT: A 348 LYS cc_start: 0.8436 (mttm) cc_final: 0.7646 (mtpt) REVERT: B 11 GLN cc_start: 0.8406 (pp30) cc_final: 0.8073 (pp30) REVERT: B 12 ILE cc_start: 0.8058 (pt) cc_final: 0.7560 (pt) REVERT: B 62 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6524 (mmm160) REVERT: B 69 LYS cc_start: 0.8366 (tttt) cc_final: 0.7933 (tptm) REVERT: B 93 VAL cc_start: 0.8422 (p) cc_final: 0.8195 (p) REVERT: C 15 LYS cc_start: 0.5778 (tttm) cc_final: 0.5499 (mttp) REVERT: C 19 LEU cc_start: 0.8634 (tp) cc_final: 0.8424 (tp) REVERT: E 56 ASP cc_start: 0.8041 (p0) cc_final: 0.7659 (p0) REVERT: E 102 MET cc_start: 0.7912 (tpt) cc_final: 0.7561 (tpt) REVERT: G 1 MET cc_start: 0.5144 (ttt) cc_final: 0.3605 (ttt) REVERT: H 14 CYS cc_start: 0.7353 (m) cc_final: 0.7064 (m) REVERT: J 21 LYS cc_start: 0.5901 (mtmt) cc_final: 0.5655 (ptpp) REVERT: J 67 LYS cc_start: 0.7828 (mttt) cc_final: 0.7263 (mttm) REVERT: J 103 GLN cc_start: 0.6163 (mm-40) cc_final: 0.5452 (mm-40) REVERT: K 40 ILE cc_start: 0.6618 (mp) cc_final: 0.6348 (mp) REVERT: K 57 MET cc_start: -0.2614 (ttm) cc_final: -0.3173 (tpt) REVERT: K 114 ILE cc_start: 0.6212 (pt) cc_final: 0.5890 (mm) REVERT: K 254 GLN cc_start: 0.6286 (tp40) cc_final: 0.5330 (mt0) REVERT: K 264 MET cc_start: 0.5771 (mtm) cc_final: 0.5567 (tmm) REVERT: K 270 ASP cc_start: 0.4381 (m-30) cc_final: 0.3914 (p0) REVERT: K 358 MET cc_start: 0.1326 (mmt) cc_final: 0.1072 (mmt) REVERT: K 393 GLN cc_start: 0.5156 (tp40) cc_final: 0.4815 (tp40) REVERT: K 520 LYS cc_start: 0.1264 (ttpp) cc_final: 0.0226 (tptt) REVERT: K 630 MET cc_start: 0.3957 (mmm) cc_final: 0.3592 (mmm) REVERT: K 637 MET cc_start: 0.1215 (tpt) cc_final: 0.0903 (tpt) REVERT: K 708 GLU cc_start: 0.4279 (pp20) cc_final: 0.3786 (pp20) REVERT: K 987 CYS cc_start: 0.6688 (m) cc_final: 0.5949 (p) REVERT: K 1015 MET cc_start: 0.0958 (mtt) cc_final: -0.1551 (tpt) REVERT: K 1021 MET cc_start: 0.2256 (mmt) cc_final: 0.1629 (ptt) REVERT: K 1091 MET cc_start: 0.4009 (mpp) cc_final: 0.3470 (mpp) REVERT: K 1117 SER cc_start: 0.5541 (m) cc_final: 0.4917 (m) REVERT: K 1118 LYS cc_start: 0.3658 (pttt) cc_final: 0.1990 (mptt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.6349 time to fit residues: 395.1790 Evaluate side-chains 313 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 310 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 712 GLN ** K 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1056 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.180029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166472 restraints weight = 112092.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167076 restraints weight = 109337.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164325 restraints weight = 57896.055| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 50134 Z= 0.290 Angle : 0.822 13.425 73347 Z= 0.416 Chirality : 0.044 0.300 9186 Planarity : 0.006 0.131 5036 Dihedral : 23.731 179.960 20801 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.93 % Allowed : 13.77 % Favored : 85.29 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.37 % 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: -3.79 (0.14), residues: 2781 helix: -0.88 (0.20), residues: 627 sheet: -2.58 (0.26), residues: 313 loop : -3.34 (0.12), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP A 258 HIS 0.009 0.002 HIS A 277 PHE 0.023 0.002 PHE B 97 TYR 0.027 0.003 TYR F 9 ARG 0.014 0.001 ARG E 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8488.98 seconds wall clock time: 156 minutes 8.25 seconds (9368.25 seconds total)