Starting phenix.real_space_refine on Fri Jan 19 16:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/01_2024/6gtc_0061.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/01_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_0061/01_2024/6gtc_0061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/01_2024/6gtc_0061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/01_2024/6gtc_0061.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/01_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 7.07, per 1000 atoms: 0.59 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: 5.58 Conformation dependent library (CDL) restraints added in 2.1 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: 4.13 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: 4.58 Time building geometry restraints manager: 5.88 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: 6817 25.06 - 50.11: 425 50.11 - 75.17: 97 75.17 - 100.23: 13 100.23 - 125.28: 1 Dihedral angle restraints: 7353 sinusoidal: 3556 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 7350 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 3.600 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.120 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.660 ------------------------------------------------------------------------------- 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 : 16.322 125.283 4899 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 : 1.599 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: 0.2862 time to fit residues: 105.3725 Evaluate side-chains 149 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 384 GLN A 395 ASN A 516 GLN A 538 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12302 Z= 0.397 Angle : 0.803 11.091 16822 Z= 0.428 Chirality : 0.049 0.234 1828 Planarity : 0.006 0.079 1925 Dihedral : 18.940 123.911 2161 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 4.38 % Allowed : 11.94 % Favored : 83.68 % 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: -4.87 (0.19), residues: 1272 helix: -3.67 (0.15), residues: 494 sheet: -3.10 (0.46), residues: 113 loop : -2.89 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 971 HIS 0.005 0.001 HIS A 990 PHE 0.030 0.003 PHE A 622 TYR 0.025 0.002 TYR A 789 ARG 0.008 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: 51 poor density : 164 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.7147 (ttm) cc_final: 0.6835 (ttm) REVERT: A 688 ILE cc_start: 0.7518 (mp) cc_final: 0.6780 (mm) REVERT: A 785 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7166 (tt) REVERT: A 888 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7553 (t80) REVERT: A 1178 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5597 (tp) REVERT: A 1222 THR cc_start: 0.2273 (OUTLIER) cc_final: 0.1695 (m) outliers start: 51 outliers final: 22 residues processed: 201 average time/residue: 0.2534 time to fit residues: 72.4684 Evaluate side-chains 172 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 578 LEU Chi-restraints excluded: chain A residue 587 THR 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: 6.9990 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 580 ASN ** 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 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12302 Z= 0.309 Angle : 0.723 16.853 16822 Z= 0.378 Chirality : 0.045 0.201 1828 Planarity : 0.005 0.077 1925 Dihedral : 18.869 126.945 2159 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 4.47 % Allowed : 15.38 % Favored : 80.15 % 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: -4.26 (0.20), residues: 1272 helix: -3.11 (0.18), residues: 489 sheet: -2.66 (0.52), residues: 94 loop : -2.65 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 971 HIS 0.005 0.001 HIS A 990 PHE 0.021 0.002 PHE A 622 TYR 0.026 0.002 TYR A 47 ARG 0.004 0.001 ARG A 18 *********************** 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 208 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6719 (mp) REVERT: A 646 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6807 (mt) REVERT: A 789 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (p90) REVERT: A 888 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7428 (t80) REVERT: A 968 ARG cc_start: 0.5833 (mmm-85) cc_final: 0.5483 (tpp80) REVERT: A 1064 PHE cc_start: 0.6695 (m-80) cc_final: 0.6446 (m-80) outliers start: 52 outliers final: 31 residues processed: 195 average time/residue: 0.2464 time to fit residues: 69.0422 Evaluate side-chains 171 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 113 ILE 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 789 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 1237 ASN Chi-restraints excluded: chain A residue 1253 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS A 745 GLN ** A 779 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** A 987 GLN A1219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12302 Z= 0.231 Angle : 0.661 12.868 16822 Z= 0.347 Chirality : 0.043 0.185 1828 Planarity : 0.004 0.073 1925 Dihedral : 18.840 128.200 2159 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.07 % Allowed : 16.32 % 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: -3.85 (0.21), residues: 1272 helix: -2.68 (0.20), residues: 501 sheet: -2.65 (0.52), residues: 100 loop : -2.42 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 141 HIS 0.004 0.001 HIS A 544 PHE 0.024 0.002 PHE A1108 TYR 0.023 0.002 TYR A 47 ARG 0.004 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 212 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5163 (pt) REVERT: A 311 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6754 (mp) REVERT: A 487 MET cc_start: 0.7194 (pmm) cc_final: 0.6904 (pmm) REVERT: A 646 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6608 (mt) REVERT: A 785 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7199 (tt) REVERT: A 789 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7522 (p90) REVERT: A 888 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7357 (t80) REVERT: A 968 ARG cc_start: 0.5766 (mmm-85) cc_final: 0.5381 (tpp80) REVERT: A 1064 PHE cc_start: 0.6503 (m-80) cc_final: 0.6286 (m-80) outliers start: 59 outliers final: 33 residues processed: 201 average time/residue: 0.2513 time to fit residues: 72.4083 Evaluate side-chains 180 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 204 VAL 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 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 785 LEU Chi-restraints excluded: chain A residue 789 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 1058 THR 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 1237 ASN Chi-restraints excluded: chain A residue 1253 ASP 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: 0.9990 chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.0000 chunk 109 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 353 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS A1106 GLN A1219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12302 Z= 0.162 Angle : 0.621 13.264 16822 Z= 0.323 Chirality : 0.041 0.172 1828 Planarity : 0.004 0.069 1925 Dihedral : 18.781 131.610 2159 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.21 % Allowed : 17.01 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.22), residues: 1272 helix: -2.39 (0.21), residues: 510 sheet: -2.18 (0.55), residues: 97 loop : -2.32 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 609 HIS 0.004 0.001 HIS A 922 PHE 0.014 0.001 PHE A 941 TYR 0.031 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 203 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6755 (mp) REVERT: A 789 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7298 (p90) REVERT: A 964 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5853 (ppt170) REVERT: A 968 ARG cc_start: 0.5737 (mmm-85) cc_final: 0.5387 (tpp80) outliers start: 49 outliers final: 26 residues processed: 189 average time/residue: 0.2532 time to fit residues: 68.8053 Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 137 ASP 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 350 THR Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 789 TYR 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 888 PHE 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 1219 ASN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1237 ASN 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: 0.0770 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- 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 384 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12302 Z= 0.430 Angle : 0.781 11.273 16822 Z= 0.408 Chirality : 0.049 0.213 1828 Planarity : 0.005 0.081 1925 Dihedral : 19.107 130.440 2159 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 5.84 % Allowed : 16.84 % Favored : 77.32 % 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: -3.63 (0.22), residues: 1272 helix: -2.41 (0.21), residues: 499 sheet: -2.39 (0.56), residues: 96 loop : -2.41 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1163 HIS 0.006 0.002 HIS A 544 PHE 0.025 0.002 PHE A 622 TYR 0.027 0.002 TYR A 11 ARG 0.006 0.001 ARG A1218 *********************** 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 212 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 144 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5344 (pt) REVERT: A 311 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6782 (mp) REVERT: A 785 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 789 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A 888 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7474 (t80) REVERT: A 968 ARG cc_start: 0.5456 (mmm-85) cc_final: 0.5056 (tpp80) REVERT: A 1023 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8269 (t) outliers start: 68 outliers final: 41 residues processed: 198 average time/residue: 0.2420 time to fit residues: 69.8123 Evaluate side-chains 183 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 113 ILE Chi-restraints excluded: chain A residue 128 ILE 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 273 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 328 ILE 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 587 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 842 THR 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 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1058 THR 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 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 1283 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** A1009 ASN A1219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12302 Z= 0.177 Angle : 0.642 12.311 16822 Z= 0.333 Chirality : 0.042 0.179 1828 Planarity : 0.004 0.069 1925 Dihedral : 18.938 133.151 2159 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.21 % Allowed : 19.33 % Favored : 76.46 % 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: -3.31 (0.22), residues: 1272 helix: -2.27 (0.21), residues: 504 sheet: -1.94 (0.61), residues: 85 loop : -2.16 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 609 HIS 0.003 0.001 HIS A 544 PHE 0.030 0.001 PHE A 941 TYR 0.024 0.001 TYR A1099 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 185 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.5111 (pt) REVERT: A 311 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6806 (mp) REVERT: A 689 LEU cc_start: 0.7955 (mm) cc_final: 0.7474 (tp) REVERT: A 789 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7503 (p90) REVERT: A 968 ARG cc_start: 0.5632 (mmm-85) cc_final: 0.5274 (tpp80) outliers start: 49 outliers final: 34 residues processed: 170 average time/residue: 0.2393 time to fit residues: 60.2910 Evaluate side-chains 172 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 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 75 LEU 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 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 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 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG 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 1120 ASP Chi-restraints excluded: chain A residue 1151 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 1267 LEU 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: 10.0000 chunk 76 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12302 Z= 0.426 Angle : 0.796 11.926 16822 Z= 0.414 Chirality : 0.049 0.212 1828 Planarity : 0.005 0.084 1925 Dihedral : 19.251 138.925 2159 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 4.73 % Allowed : 18.47 % Favored : 76.80 % 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: -3.65 (0.22), residues: 1272 helix: -2.42 (0.20), residues: 510 sheet: -2.58 (0.53), residues: 103 loop : -2.37 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1163 HIS 0.007 0.002 HIS A1261 PHE 0.038 0.002 PHE A 941 TYR 0.026 0.002 TYR A 11 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 185 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 130 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6817 (mp) REVERT: A 785 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7175 (tt) REVERT: A 789 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7581 (p90) REVERT: A 888 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7484 (t80) outliers start: 55 outliers final: 40 residues processed: 172 average time/residue: 0.2486 time to fit residues: 62.8775 Evaluate side-chains 167 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 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 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 842 THR 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 888 PHE 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 942 ASN 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 1058 THR 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 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 1253 ASP Chi-restraints excluded: chain A residue 1267 LEU 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: 2.9990 chunk 112 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.7053 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12302 Z= 0.270 Angle : 0.707 18.560 16822 Z= 0.364 Chirality : 0.045 0.190 1828 Planarity : 0.004 0.071 1925 Dihedral : 19.122 139.848 2159 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.47 % Allowed : 19.07 % Favored : 76.46 % 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: -3.38 (0.22), residues: 1272 helix: -2.27 (0.21), residues: 509 sheet: -2.24 (0.59), residues: 86 loop : -2.21 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 609 HIS 0.004 0.001 HIS A 544 PHE 0.035 0.002 PHE A 941 TYR 0.024 0.002 TYR A 47 ARG 0.003 0.000 ARG A 202 *********************** 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 184 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 132 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6832 (mp) REVERT: A 785 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7159 (tt) REVERT: A 789 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7487 (p90) REVERT: A 1221 LYS cc_start: 0.5558 (tptp) cc_final: 0.5342 (tptp) outliers start: 52 outliers final: 44 residues processed: 171 average time/residue: 0.2561 time to fit residues: 63.6702 Evaluate side-chains 176 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 129 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain A residue 374 LEU 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 627 LYS Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 825 ASN 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 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 942 ASN Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1009 ASN Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1058 THR 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 1207 LEU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1219 ASN 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 1267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.0010 chunk 87 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 353 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12302 Z= 0.168 Angle : 0.644 18.747 16822 Z= 0.332 Chirality : 0.042 0.178 1828 Planarity : 0.004 0.067 1925 Dihedral : 18.990 140.741 2159 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.52 % Allowed : 20.36 % Favored : 76.12 % 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: -3.09 (0.22), residues: 1272 helix: -2.00 (0.22), residues: 507 sheet: -1.82 (0.61), residues: 85 loop : -2.11 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 609 HIS 0.004 0.001 HIS A 731 PHE 0.031 0.001 PHE A 888 TYR 0.042 0.001 TYR A1099 ARG 0.011 0.001 ARG A1218 ********************** 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 174 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6794 (mp) REVERT: A 345 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A 353 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7775 (pp30) REVERT: A 689 LEU cc_start: 0.7966 (mm) cc_final: 0.7495 (tp) REVERT: A 785 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7092 (tt) REVERT: A 964 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.5807 (ppt170) outliers start: 41 outliers final: 29 residues processed: 164 average time/residue: 0.2378 time to fit residues: 57.8568 Evaluate side-chains 161 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 374 LEU 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 785 LEU Chi-restraints excluded: chain A residue 825 ASN 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 913 ILE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 964 ARG Chi-restraints excluded: chain A residue 1009 ASN 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 1120 ASP Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1211 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 29 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 108 optimal weight: 0.1980 chunk 13 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 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** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.172575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143050 restraints weight = 16958.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143287 restraints weight = 19580.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145822 restraints weight = 17097.488| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 12302 Z= 0.314 Angle : 0.893 59.089 16822 Z= 0.499 Chirality : 0.047 0.941 1828 Planarity : 0.004 0.067 1925 Dihedral : 18.987 140.727 2159 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.09 % Allowed : 21.22 % Favored : 75.69 % Cbeta Deviations : 0.08 % 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: -1.98 (0.22), residues: 507 sheet: -1.79 (0.61), residues: 85 loop : -2.11 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 609 HIS 0.004 0.001 HIS A 731 PHE 0.028 0.001 PHE A 888 TYR 0.054 0.002 TYR A 925 ARG 0.004 0.000 ARG A1218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.13 seconds wall clock time: 45 minutes 47.87 seconds (2747.87 seconds total)