Starting phenix.real_space_refine on Sat Dec 9 18:30:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/12_2023/6gtc_0061.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/12_2023/6gtc_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_0061/12_2023/6gtc_0061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/12_2023/6gtc_0061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/12_2023/6gtc_0061.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtc_0061/12_2023/6gtc_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-1.21rc1-5172/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: 6.93, per 1000 atoms: 0.58 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: 5.01 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: 3.94 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: 4.54 Time building geometry restraints manager: 5.36 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.530 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.880 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- 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 : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 268 average time/residue: 0.2779 time to fit residues: 102.1084 Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 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: 0.7054 moved from start: 0.3081 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 : 0.797 11.615 16822 Z= 0.424 Chirality : 0.049 0.241 1828 Planarity : 0.006 0.079 1925 Dihedral : 18.885 125.182 2159 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 3.95 % Allowed : 12.37 % 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: -4.91 (0.19), residues: 1272 helix: -3.70 (0.15), residues: 495 sheet: -3.09 (0.47), residues: 113 loop : -2.92 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 971 HIS 0.005 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 212 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 200 average time/residue: 0.2709 time to fit residues: 77.2889 Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1239 time to fit residues: 6.7812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.5442 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12302 Z= 0.292 Angle : 0.724 17.935 16822 Z= 0.376 Chirality : 0.045 0.211 1828 Planarity : 0.005 0.077 1925 Dihedral : 18.841 126.658 2159 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 2.92 % Allowed : 15.98 % Favored : 81.10 % 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: -4.22 (0.20), residues: 1272 helix: -3.07 (0.18), residues: 489 sheet: -2.61 (0.53), residues: 94 loop : -2.63 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 971 HIS 0.004 0.001 HIS A 694 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 190 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 181 average time/residue: 0.2608 time to fit residues: 67.5282 Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1704 time to fit residues: 5.7996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS A 779 ASN ** 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** A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12302 Z= 0.180 Angle : 0.630 14.024 16822 Z= 0.331 Chirality : 0.042 0.179 1828 Planarity : 0.004 0.072 1925 Dihedral : 18.775 128.141 2159 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.01 % Allowed : 17.10 % Favored : 79.90 % 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: -3.84 (0.21), residues: 1272 helix: -2.69 (0.19), residues: 504 sheet: -2.43 (0.53), residues: 96 loop : -2.44 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1163 HIS 0.004 0.001 HIS A 922 PHE 0.025 0.001 PHE A 941 TYR 0.020 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 192 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 184 average time/residue: 0.2436 time to fit residues: 67.6168 Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1170 time to fit residues: 4.9353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 312 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6924 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12302 Z= 0.198 Angle : 0.634 12.250 16822 Z= 0.330 Chirality : 0.042 0.232 1828 Planarity : 0.004 0.070 1925 Dihedral : 18.770 130.905 2159 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.98 % Allowed : 19.33 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.51 (0.22), residues: 1272 helix: -2.33 (0.21), residues: 501 sheet: -2.16 (0.55), residues: 96 loop : -2.35 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 141 HIS 0.004 0.001 HIS A 544 PHE 0.030 0.001 PHE A 941 TYR 0.026 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 175 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 167 average time/residue: 0.2472 time to fit residues: 60.8081 Evaluate side-chains 149 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1827 time to fit residues: 4.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 0.1980 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.4484 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12302 Z= 0.289 Angle : 0.685 11.320 16822 Z= 0.357 Chirality : 0.044 0.205 1828 Planarity : 0.004 0.069 1925 Dihedral : 18.931 130.514 2159 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.58 % Allowed : 19.76 % Favored : 77.66 % 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: -3.47 (0.22), residues: 1272 helix: -2.29 (0.21), residues: 501 sheet: -2.23 (0.55), residues: 96 loop : -2.31 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 141 HIS 0.005 0.001 HIS A 694 PHE 0.025 0.002 PHE A 941 TYR 0.021 0.002 TYR A 11 ARG 0.004 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 177 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 169 average time/residue: 0.2307 time to fit residues: 57.8127 Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1136 time to fit residues: 4.8212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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** ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4415 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= 0.285 Angle : 0.687 11.400 16822 Z= 0.358 Chirality : 0.045 0.182 1828 Planarity : 0.004 0.070 1925 Dihedral : 18.997 136.078 2159 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.23 % Allowed : 19.67 % Favored : 78.09 % 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: -3.32 (0.22), residues: 1272 helix: -2.15 (0.21), residues: 506 sheet: -2.16 (0.56), residues: 96 loop : -2.24 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 609 HIS 0.005 0.001 HIS A 544 PHE 0.026 0.002 PHE A 941 TYR 0.020 0.002 TYR A 11 ARG 0.004 0.000 ARG A 202 *********************** 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 170 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 161 average time/residue: 0.2577 time to fit residues: 61.6247 Evaluate side-chains 148 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1163 time to fit residues: 4.9771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 649 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12302 Z= 0.331 Angle : 0.738 21.673 16822 Z= 0.380 Chirality : 0.047 0.298 1828 Planarity : 0.004 0.070 1925 Dihedral : 19.137 139.712 2159 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 1.63 % Allowed : 20.70 % Favored : 77.66 % 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: -3.46 (0.22), residues: 1272 helix: -2.24 (0.21), residues: 511 sheet: -2.27 (0.56), residues: 96 loop : -2.32 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 609 HIS 0.005 0.001 HIS A 544 PHE 0.030 0.002 PHE A 941 TYR 0.022 0.002 TYR A 11 ARG 0.004 0.001 ARG A 202 *********************** 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 154 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.2369 time to fit residues: 51.3199 Evaluate side-chains 133 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1123 time to fit residues: 3.7888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 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** A 938 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12302 Z= 0.185 Angle : 0.657 20.497 16822 Z= 0.334 Chirality : 0.042 0.215 1828 Planarity : 0.004 0.067 1925 Dihedral : 19.001 140.519 2159 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.52 % Allowed : 21.82 % Favored : 77.66 % 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: -3.13 (0.22), residues: 1272 helix: -2.02 (0.21), residues: 515 sheet: -1.71 (0.62), residues: 83 loop : -2.16 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 609 HIS 0.008 0.001 HIS A 694 PHE 0.032 0.001 PHE A 888 TYR 0.022 0.001 TYR A1099 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 143 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.333 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 138 average time/residue: 0.2495 time to fit residues: 50.3560 Evaluate side-chains 133 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1222 time to fit residues: 2.8647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12302 Z= 0.246 Angle : 0.683 20.215 16822 Z= 0.349 Chirality : 0.044 0.249 1828 Planarity : 0.004 0.067 1925 Dihedral : 19.059 142.217 2159 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.26 % Allowed : 22.59 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1272 helix: -1.98 (0.21), residues: 522 sheet: -1.75 (0.60), residues: 85 loop : -2.21 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 609 HIS 0.005 0.001 HIS A 694 PHE 0.031 0.002 PHE A 888 TYR 0.020 0.002 TYR A 11 ARG 0.004 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 127 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.314 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 125 average time/residue: 0.2653 time to fit residues: 48.1870 Evaluate side-chains 127 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1074 time to fit residues: 2.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.0670 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 108 optimal weight: 0.0020 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3326 ------------------------------------------------------------------------------- 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 ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 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** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147947 restraints weight = 16626.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147036 restraints weight = 18341.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148546 restraints weight = 17886.764| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12302 Z= 0.149 Angle : 0.628 20.120 16822 Z= 0.319 Chirality : 0.041 0.182 1828 Planarity : 0.003 0.066 1925 Dihedral : 18.933 142.851 2159 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.34 % Allowed : 22.34 % 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: -2.80 (0.22), residues: 1272 helix: -1.66 (0.22), residues: 510 sheet: -0.70 (0.76), residues: 65 loop : -2.15 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 609 HIS 0.005 0.001 HIS A 731 PHE 0.028 0.001 PHE A 888 TYR 0.031 0.001 TYR A1099 ARG 0.003 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.30 seconds wall clock time: 43 minutes 41.78 seconds (2621.78 seconds total)