Starting phenix.real_space_refine on Fri Mar 15 14:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/03_2024/6gtc_0061.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 65 5.49 5 S 22 5.16 5 C 7423 2.51 5 N 1994 2.21 5 O 2427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11931 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 10575 Classifications: {'peptide': 1280} Link IDs: {'PTRANS': 27, 'TRANS': 1252} Chain breaks: 3 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 8, 'rna3p': 19} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Time building chain proxies: 6.75, per 1000 atoms: 0.57 Number of scatterers: 11931 At special positions: 0 Unit cell: (94.016, 124.8, 110.656, 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 22 16.00 P 65 15.00 O 2427 8.00 N 1994 7.00 C 7423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 38.0% alpha, 7.7% beta 5 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.562A pdb=" N GLN A 5 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 6 " --> pdb=" O ILE A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 6' Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.850A pdb=" N ASN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.700A pdb=" N GLU A 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.799A pdb=" N ASP A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.747A pdb=" N TYR A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.724A pdb=" N THR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.806A pdb=" N LYS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.749A pdb=" N LEU A 127 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 4.018A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.555A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.580A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.663A pdb=" N ALA A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 removed outlier: 3.690A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 3.615A pdb=" N ILE A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.689A pdb=" N TYR A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLN A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 removed outlier: 3.776A pdb=" N LEU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.635A pdb=" N LEU A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.817A pdb=" N LEU A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.532A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.607A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.964A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 565 removed outlier: 3.851A pdb=" N VAL A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.851A pdb=" N ASN A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.632A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 683 removed outlier: 3.773A pdb=" N TYR A 682 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 683 " --> pdb=" O LYS A 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 683' Processing helix chain 'A' and resid 685 through 695 removed outlier: 4.812A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 718 removed outlier: 3.964A pdb=" N ARG A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 718' Processing helix chain 'A' and resid 719 through 729 Processing helix chain 'A' and resid 743 through 747 removed outlier: 3.792A pdb=" N TYR A 747 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 758 removed outlier: 3.663A pdb=" N ARG A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.917A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 808 through 811 Processing helix chain 'A' and resid 813 through 819 removed outlier: 4.266A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.574A pdb=" N ASN A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 removed outlier: 4.129A pdb=" N GLU A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 908 " --> pdb=" O LYS A 905 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN A 909 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 911 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 959 Processing helix chain 'A' and resid 970 through 994 removed outlier: 3.790A pdb=" N ILE A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 978 " --> pdb=" O ILE A 974 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1021 through 1026 removed outlier: 3.785A pdb=" N GLN A1025 " --> pdb=" O LYS A1021 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A1026 " --> pdb=" O GLN A1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1021 through 1026' Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.713A pdb=" N GLY A1068 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1112 removed outlier: 3.914A pdb=" N GLU A1107 " --> pdb=" O SER A1103 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A1112 " --> pdb=" O PHE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.688A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1133 " --> pdb=" O TYR A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1129 through 1133' Processing helix chain 'A' and resid 1169 through 1180 Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.530A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.853A pdb=" N PHE A1204 " --> pdb=" O ASP A1200 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A1208 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.790A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1275 removed outlier: 3.779A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1270 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 3.691A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.567A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 20 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 788 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.567A pdb=" N LYS A 877 " --> pdb=" O ARG A 833 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.912A pdb=" N PHE A 244 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG A 256 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 removed outlier: 4.037A pdb=" N LYS A 288 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 297 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR A 295 " --> pdb=" O VAL A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 661 removed outlier: 3.621A pdb=" N THR A 765 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 841 through 843 Processing sheet with id=AA8, first strand: chain 'A' and resid 927 through 929 removed outlier: 7.211A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 943 through 944 Processing sheet with id=AB1, first strand: chain 'A' and resid 1003 through 1006 removed outlier: 6.788A pdb=" N VAL A1003 " --> pdb=" O TYR A1075 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A1077 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A1005 " --> pdb=" O VAL A1077 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 3.700A pdb=" N LYS A1114 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1150 through 1153 removed outlier: 3.758A pdb=" N ARG A1150 " --> pdb=" O VAL A1168 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A1168 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A1152 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A1166 " --> pdb=" O ILE A1152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1219 through 1220 removed outlier: 4.334A pdb=" N ASN A1219 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A1228 " --> pdb=" O ASN A1219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 231 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3054 1.33 - 1.45: 2553 1.45 - 1.57: 6533 1.57 - 1.69: 127 1.69 - 1.81: 35 Bond restraints: 12302 Sorted by residual: bond pdb=" C VAL A 576 " pdb=" N PRO A 577 " ideal model delta sigma weight residual 1.331 1.400 -0.068 7.90e-03 1.60e+04 7.51e+01 bond pdb=" C VAL A1168 " pdb=" N TYR A1169 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.07e-02 2.33e+03 1.22e+01 bond pdb=" CA LYS A1034 " pdb=" CB LYS A1034 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.39e-02 5.18e+03 4.84e+00 bond pdb=" C3' DG C -7 " pdb=" O3' DG C -7 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CA ASP A 947 " pdb=" C ASP A 947 " ideal model delta sigma weight residual 1.522 1.555 -0.034 1.72e-02 3.38e+03 3.84e+00 ... (remaining 12297 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.13: 501 106.13 - 113.43: 6482 113.43 - 120.74: 5627 120.74 - 128.05: 4071 128.05 - 135.35: 141 Bond angle restraints: 16822 Sorted by residual: angle pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" C ILE A 105 " ideal model delta sigma weight residual 113.53 107.60 5.93 9.80e-01 1.04e+00 3.66e+01 angle pdb=" N VAL A 523 " pdb=" CA VAL A 523 " pdb=" C VAL A 523 " ideal model delta sigma weight residual 112.96 107.00 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" N ILE A 65 " pdb=" CA ILE A 65 " pdb=" C ILE A 65 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" C LYS A 869 " pdb=" N ASP A 870 " pdb=" CA ASP A 870 " ideal model delta sigma weight residual 121.54 131.17 -9.63 1.91e+00 2.74e-01 2.54e+01 angle pdb=" N ILE A 913 " pdb=" CA ILE A 913 " pdb=" C ILE A 913 " ideal model delta sigma weight residual 108.93 115.48 -6.55 1.35e+00 5.49e-01 2.36e+01 ... (remaining 16817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 6837 25.06 - 50.11: 435 50.11 - 75.17: 107 75.17 - 100.23: 13 100.23 - 125.28: 1 Dihedral angle restraints: 7393 sinusoidal: 3596 harmonic: 3797 Sorted by residual: dihedral pdb=" CA GLU A 614 " pdb=" C GLU A 614 " pdb=" N PRO A 615 " pdb=" CA PRO A 615 " ideal model delta harmonic sigma weight residual 180.00 144.40 35.60 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA ASN A 617 " pdb=" C ASN A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 7390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1737 0.105 - 0.210: 84 0.210 - 0.315: 5 0.315 - 0.420: 1 0.420 - 0.525: 1 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CB ILE A1002 " pdb=" CA ILE A1002 " pdb=" CG1 ILE A1002 " pdb=" CG2 ILE A1002 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CB ILE A1074 " pdb=" CA ILE A1074 " pdb=" CG1 ILE A1074 " pdb=" CG2 ILE A1074 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB VAL A 576 " pdb=" CA VAL A 576 " pdb=" CG1 VAL A 576 " pdb=" CG2 VAL A 576 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1825 not shown) Planarity restraints: 1925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 614 " 0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 615 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 615 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 615 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 670 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 272 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C TYR A 272 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 272 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A 273 " 0.019 2.00e-02 2.50e+03 ... (remaining 1922 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3158 2.80 - 3.32: 10135 3.32 - 3.85: 19859 3.85 - 4.37: 23088 4.37 - 4.90: 37513 Nonbonded interactions: 93753 Sorted by model distance: nonbonded pdb=" OD1 ASN A 825 " pdb=" OG1 THR A 885 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR A 83 " pdb=" O PRO A 209 " model vdw 2.278 2.440 nonbonded pdb=" O PHE A 941 " pdb=" OH TYR A 984 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR A 392 " pdb=" OD1 ASP A 556 " model vdw 2.301 2.440 nonbonded pdb=" O LEU A 418 " pdb=" OG1 THR A 422 " model vdw 2.316 2.440 ... (remaining 93748 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.010 Extract box with map and model: 3.510 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12302 Z= 0.266 Angle : 0.945 15.978 16822 Z= 0.504 Chirality : 0.054 0.525 1828 Planarity : 0.006 0.090 1925 Dihedral : 16.563 125.283 4939 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.86 % Allowed : 7.73 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -5.69 (0.16), residues: 1272 helix: -4.79 (0.08), residues: 474 sheet: -2.79 (0.51), residues: 95 loop : -3.23 (0.18), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 971 HIS 0.008 0.002 HIS A 544 PHE 0.027 0.002 PHE A 258 TYR 0.021 0.002 TYR A 272 ARG 0.007 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 259 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 ILE cc_start: 0.7326 (mp) cc_final: 0.6608 (mm) REVERT: A 920 GLU cc_start: 0.4849 (mt-10) cc_final: 0.4204 (mt-10) REVERT: A 1027 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (tt) outliers start: 10 outliers final: 0 residues processed: 268 average time/residue: 0.2787 time to fit residues: 102.3028 Evaluate side-chains 149 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 77 GLN A 78 ASN A 126 ASN A 185 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 516 GLN A 538 HIS A 580 ASN A 588 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 HIS A 851 ASN A 853 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12302 Z= 0.393 Angle : 0.796 11.440 16822 Z= 0.424 Chirality : 0.049 0.239 1828 Planarity : 0.006 0.079 1925 Dihedral : 19.289 124.035 2201 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 4.12 % Allowed : 12.29 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.19), residues: 1272 helix: -3.69 (0.15), residues: 495 sheet: -3.08 (0.47), residues: 113 loop : -2.90 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 971 HIS 0.004 0.001 HIS A 990 PHE 0.030 0.003 PHE A 622 TYR 0.022 0.002 TYR A 11 ARG 0.007 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.7107 (ttm) cc_final: 0.6775 (ttm) REVERT: A 688 ILE cc_start: 0.7495 (mp) cc_final: 0.6785 (mm) REVERT: A 785 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7101 (tt) REVERT: A 888 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 1178 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5663 (tp) REVERT: A 1217 MET cc_start: 0.5444 (mmp) cc_final: 0.5216 (mmt) REVERT: A 1222 THR cc_start: 0.2355 (OUTLIER) cc_final: 0.1766 (m) outliers start: 48 outliers final: 22 residues processed: 202 average time/residue: 0.2544 time to fit residues: 73.1463 Evaluate side-chains 168 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1222 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 538 HIS ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12302 Z= 0.263 Angle : 0.696 16.776 16822 Z= 0.364 Chirality : 0.044 0.215 1828 Planarity : 0.005 0.076 1925 Dihedral : 19.209 127.332 2199 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.87 % Allowed : 15.72 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -4.25 (0.20), residues: 1272 helix: -3.11 (0.18), residues: 495 sheet: -2.58 (0.52), residues: 94 loop : -2.65 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 971 HIS 0.004 0.001 HIS A 990 PHE 0.022 0.002 PHE A 941 TYR 0.025 0.002 TYR A 47 ARG 0.005 0.001 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7440 (p90) REVERT: A 311 ILE cc_start: 0.7113 (OUTLIER) cc_final: 0.6725 (mp) REVERT: A 646 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6756 (mt) REVERT: A 888 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7417 (t80) REVERT: A 943 ILE cc_start: 0.6539 (mm) cc_final: 0.6300 (mt) REVERT: A 964 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5767 (ppt170) REVERT: A 968 ARG cc_start: 0.5781 (mmm-85) cc_final: 0.5439 (tpp80) REVERT: A 1064 PHE cc_start: 0.6581 (m-80) cc_final: 0.6376 (m-80) outliers start: 45 outliers final: 27 residues processed: 191 average time/residue: 0.2510 time to fit residues: 69.1601 Evaluate side-chains 172 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1192 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 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 305 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS A 745 GLN A 779 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12302 Z= 0.170 Angle : 0.621 12.421 16822 Z= 0.327 Chirality : 0.041 0.178 1828 Planarity : 0.004 0.072 1925 Dihedral : 19.177 130.972 2199 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 3.95 % Allowed : 17.01 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.21), residues: 1272 helix: -2.62 (0.20), residues: 505 sheet: -2.30 (0.54), residues: 95 loop : -2.42 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1163 HIS 0.004 0.001 HIS A 922 PHE 0.025 0.001 PHE A1108 TYR 0.022 0.001 TYR A 47 ARG 0.003 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5257 (pt) REVERT: A 311 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6780 (mp) REVERT: A 789 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7426 (p90) REVERT: A 964 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.5831 (ppt170) REVERT: A 968 ARG cc_start: 0.5821 (mmm-85) cc_final: 0.5443 (tpp80) outliers start: 46 outliers final: 21 residues processed: 193 average time/residue: 0.2336 time to fit residues: 65.2934 Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 109 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12302 Z= 0.149 Angle : 0.602 13.530 16822 Z= 0.312 Chirality : 0.041 0.179 1828 Planarity : 0.004 0.067 1925 Dihedral : 19.198 134.094 2199 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.78 % Allowed : 17.61 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.22), residues: 1272 helix: -2.27 (0.21), residues: 510 sheet: -1.88 (0.56), residues: 97 loop : -2.31 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 141 HIS 0.003 0.001 HIS A 544 PHE 0.014 0.001 PHE A 941 TYR 0.030 0.001 TYR A 506 ARG 0.003 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6769 (tp) REVERT: A 294 ASN cc_start: 0.7834 (t0) cc_final: 0.7630 (t0) REVERT: A 311 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6760 (mp) REVERT: A 689 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7388 (tp) REVERT: A 785 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7070 (tt) REVERT: A 789 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7371 (p90) REVERT: A 964 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.5861 (ppt170) REVERT: A 968 ARG cc_start: 0.5775 (mmm-85) cc_final: 0.5409 (tpp80) REVERT: A 1031 LEU cc_start: 0.7856 (tt) cc_final: 0.7642 (tt) outliers start: 44 outliers final: 22 residues processed: 185 average time/residue: 0.2360 time to fit residues: 63.5465 Evaluate side-chains 162 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12302 Z= 0.243 Angle : 0.641 11.633 16822 Z= 0.335 Chirality : 0.043 0.173 1828 Planarity : 0.004 0.065 1925 Dihedral : 19.303 134.178 2199 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.47 % Allowed : 18.47 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.22), residues: 1272 helix: -2.14 (0.21), residues: 505 sheet: -2.00 (0.55), residues: 97 loop : -2.22 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 141 HIS 0.004 0.001 HIS A 544 PHE 0.031 0.002 PHE A 182 TYR 0.023 0.001 TYR A 47 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5328 (pt) REVERT: A 285 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 311 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6761 (mp) REVERT: A 689 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7381 (tp) REVERT: A 785 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7209 (tt) REVERT: A 964 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.5799 (ppt170) REVERT: A 1177 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7052 (tm) outliers start: 52 outliers final: 34 residues processed: 178 average time/residue: 0.2322 time to fit residues: 60.6374 Evaluate side-chains 171 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 chunk 78 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12302 Z= 0.163 Angle : 0.607 12.236 16822 Z= 0.316 Chirality : 0.041 0.180 1828 Planarity : 0.004 0.065 1925 Dihedral : 19.324 134.166 2199 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.87 % Allowed : 19.07 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1272 helix: -1.99 (0.22), residues: 510 sheet: -1.62 (0.58), residues: 95 loop : -2.12 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 609 HIS 0.003 0.001 HIS A 544 PHE 0.023 0.001 PHE A 182 TYR 0.022 0.001 TYR A 47 ARG 0.003 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 134 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6795 (mp) REVERT: A 689 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7396 (tp) REVERT: A 785 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7188 (tt) REVERT: A 964 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5762 (ppt170) REVERT: A 1177 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7018 (tm) outliers start: 45 outliers final: 27 residues processed: 168 average time/residue: 0.2300 time to fit residues: 57.1657 Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1217 MET Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN A1219 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12302 Z= 0.366 Angle : 0.737 18.043 16822 Z= 0.382 Chirality : 0.047 0.200 1828 Planarity : 0.004 0.066 1925 Dihedral : 19.559 139.630 2199 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 4.90 % Allowed : 18.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.22), residues: 1272 helix: -2.12 (0.21), residues: 506 sheet: -2.46 (0.52), residues: 109 loop : -2.24 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 609 HIS 0.008 0.002 HIS A 694 PHE 0.063 0.002 PHE A1128 TYR 0.025 0.002 TYR A1099 ARG 0.004 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 136 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 785 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7190 (tt) REVERT: A 964 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.5749 (ppt170) REVERT: A 1177 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7223 (tm) outliers start: 57 outliers final: 43 residues processed: 179 average time/residue: 0.2220 time to fit residues: 59.0460 Evaluate side-chains 170 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1219 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12302 Z= 0.191 Angle : 0.639 17.679 16822 Z= 0.330 Chirality : 0.042 0.211 1828 Planarity : 0.004 0.068 1925 Dihedral : 19.431 140.299 2199 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.87 % Allowed : 20.36 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1272 helix: -1.93 (0.22), residues: 514 sheet: -2.19 (0.54), residues: 109 loop : -2.06 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 609 HIS 0.008 0.001 HIS A 990 PHE 0.046 0.002 PHE A1128 TYR 0.023 0.001 TYR A 47 ARG 0.005 0.000 ARG A1218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 689 LEU cc_start: 0.7827 (mm) cc_final: 0.7504 (tp) REVERT: A 785 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7186 (tt) REVERT: A 789 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (p90) REVERT: A 1177 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7150 (tm) outliers start: 45 outliers final: 34 residues processed: 160 average time/residue: 0.2400 time to fit residues: 56.8798 Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1217 MET Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12302 Z= 0.179 Angle : 0.627 17.422 16822 Z= 0.322 Chirality : 0.042 0.188 1828 Planarity : 0.004 0.062 1925 Dihedral : 19.409 142.316 2199 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.52 % Allowed : 21.13 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.23), residues: 1272 helix: -1.79 (0.22), residues: 516 sheet: -1.88 (0.58), residues: 97 loop : -2.02 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 609 HIS 0.011 0.001 HIS A 990 PHE 0.040 0.001 PHE A1128 TYR 0.024 0.001 TYR A1099 ARG 0.003 0.000 ARG A 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 689 LEU cc_start: 0.7819 (mm) cc_final: 0.7494 (tp) REVERT: A 785 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7107 (tt) REVERT: A 789 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7543 (p90) REVERT: A 964 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5868 (ppt170) REVERT: A 1177 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7056 (tm) outliers start: 41 outliers final: 36 residues processed: 156 average time/residue: 0.2195 time to fit residues: 51.0815 Evaluate side-chains 160 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 556 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 683 ASN Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1071 THR Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1120 ASP Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain A residue 1262 ILE Chi-restraints excluded: chain A residue 1283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143950 restraints weight = 16684.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143847 restraints weight = 21085.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145682 restraints weight = 18972.970| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12302 Z= 0.179 Angle : 0.624 17.178 16822 Z= 0.319 Chirality : 0.041 0.180 1828 Planarity : 0.004 0.065 1925 Dihedral : 19.373 143.906 2199 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.69 % Allowed : 21.22 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1272 helix: -1.66 (0.22), residues: 518 sheet: -1.07 (0.74), residues: 65 loop : -2.06 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 609 HIS 0.010 0.001 HIS A 990 PHE 0.036 0.001 PHE A1128 TYR 0.021 0.001 TYR A 47 ARG 0.004 0.000 ARG A 872 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.64 seconds wall clock time: 43 minutes 22.16 seconds (2602.16 seconds total)