Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 13:42:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jb7_6404/08_2023/3jb7_6404_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.095 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 20 5.49 5 S 54 5.16 5 C 8939 2.51 5 N 2430 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 993": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A ARG 1079": "NH1" <-> "NH2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1145": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 14176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1198, 9561 Classifications: {'peptide': 1198} Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 35, 'TRANS': 1145} Chain breaks: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 170 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "t" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 138 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 6} Link IDs: {'rna3p': 5} Chain: "m" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna3p_pyr': 5} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CTP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.59, per 1000 atoms: 0.54 Number of scatterers: 14176 At special positions: 0 Unit cell: (103.36, 133.28, 108.8, 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 54 16.00 P 20 15.00 O 2733 8.00 N 2430 7.00 C 8939 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: 5.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 15 sheets defined 46.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.599A pdb=" N HIS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.605A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 145 through 160 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.924A pdb=" N TYR A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.636A pdb=" N VAL A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 237 removed outlier: 3.716A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.876A pdb=" N LYS A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.767A pdb=" N GLN A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 261 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.739A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.607A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.026A pdb=" N ASP A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.890A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASP A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.619A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.569A pdb=" N LYS A 468 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 471 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.476A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.647A pdb=" N GLN A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 5.058A pdb=" N GLU A 531 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 536 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 removed outlier: 4.063A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.556A pdb=" N VAL A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.646A pdb=" N TYR A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 766 removed outlier: 3.508A pdb=" N GLU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 762 " --> pdb=" O MET A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 785 removed outlier: 3.584A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 810 removed outlier: 4.562A pdb=" N TYR A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 809 " --> pdb=" O TYR A 805 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS A 810 " --> pdb=" O ASN A 806 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 810' Processing helix chain 'A' and resid 834 through 837 Processing helix chain 'A' and resid 868 through 879 removed outlier: 3.541A pdb=" N VAL A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 886 removed outlier: 4.001A pdb=" N GLN A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.765A pdb=" N GLU A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 900 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 909 removed outlier: 3.832A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 908 " --> pdb=" O GLY A 904 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 removed outlier: 3.906A pdb=" N ASP A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 941 removed outlier: 4.430A pdb=" N THR A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 941 " --> pdb=" O LEU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 956 removed outlier: 3.691A pdb=" N ASP A 955 " --> pdb=" O ARG A 951 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 removed outlier: 5.121A pdb=" N GLN A 974 " --> pdb=" O TYR A 971 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 975 " --> pdb=" O GLY A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.049A pdb=" N THR A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 996 No H-bonds generated for 'chain 'A' and resid 994 through 996' Processing helix chain 'A' and resid 1000 through 1003 No H-bonds generated for 'chain 'A' and resid 1000 through 1003' Processing helix chain 'A' and resid 1014 through 1020 removed outlier: 3.621A pdb=" N ALA A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1018 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A1019 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1039 removed outlier: 3.539A pdb=" N THR A1039 " --> pdb=" O ALA A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1048 No H-bonds generated for 'chain 'A' and resid 1046 through 1048' Processing helix chain 'A' and resid 1053 through 1061 removed outlier: 3.774A pdb=" N PHE A1058 " --> pdb=" O GLY A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1079 removed outlier: 3.964A pdb=" N ASP A1074 " --> pdb=" O LEU A1070 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1078 " --> pdb=" O ASP A1074 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1094 No H-bonds generated for 'chain 'A' and resid 1091 through 1094' Processing helix chain 'A' and resid 1096 through 1100 Processing helix chain 'A' and resid 1103 through 1113 removed outlier: 3.836A pdb=" N ASN A1107 " --> pdb=" O THR A1104 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A1112 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 removed outlier: 3.643A pdb=" N LEU A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1160 removed outlier: 3.917A pdb=" N ARG A1159 " --> pdb=" O SER A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1174 through 1187 removed outlier: 3.927A pdb=" N TYR A1177 " --> pdb=" O ARG A1174 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A1178 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1182 " --> pdb=" O ILE A1179 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU A1183 " --> pdb=" O PHE A1180 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A1185 " --> pdb=" O TYR A1182 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A1186 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1210 removed outlier: 3.786A pdb=" N ALA A1207 " --> pdb=" O PRO A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.650A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.634A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 132 through 148 removed outlier: 5.366A pdb=" N ALA B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.700A pdb=" N LEU B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.535A pdb=" N GLN B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.605A pdb=" N SER B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.737A pdb=" N PHE B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.616A pdb=" N ALA B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 374 removed outlier: 4.230A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.601A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.523A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.776A pdb=" N HIS B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 442 through 460 removed outlier: 3.527A pdb=" N MET B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 492 through 495 Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.614A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.746A pdb=" N PHE B 529 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 536 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.621A pdb=" N ARG B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.546A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.657A pdb=" N ARG A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.829A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 541 through 544 Processing sheet with id= E, first strand: chain 'A' and resid 585 through 589 Processing sheet with id= F, first strand: chain 'A' and resid 621 through 624 removed outlier: 3.665A pdb=" N GLY A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 795 through 797 removed outlier: 3.630A pdb=" N VAL A 796 " --> pdb=" O THR A 826 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1022 through 1025 removed outlier: 3.578A pdb=" N GLU A1022 " --> pdb=" O VAL A1200 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.700A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.803A pdb=" N LYS A 382 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 157 through 159 removed outlier: 6.392A pdb=" N HIS B 182 " --> pdb=" O ILE B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 204 through 208 Processing sheet with id= M, first strand: chain 'B' and resid 255 through 258 removed outlier: 3.590A pdb=" N SER B 317 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= O, first strand: chain 'B' and resid 485 through 489 417 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 730 1.23 - 1.38: 4749 1.38 - 1.53: 8094 1.53 - 1.68: 832 1.68 - 1.83: 95 Bond restraints: 14500 Sorted by residual: bond pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta sigma weight residual 1.466 1.114 0.352 1.50e-02 4.44e+03 5.52e+02 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.233 1.087 0.146 1.13e-02 7.83e+03 1.67e+02 bond pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 1.540 1.401 0.138 1.10e-02 8.26e+03 1.59e+02 bond pdb=" CA PRO C 132 " pdb=" C PRO C 132 " ideal model delta sigma weight residual 1.522 1.383 0.139 1.16e-02 7.43e+03 1.43e+02 bond pdb=" N PRO D 111 " pdb=" CD PRO D 111 " ideal model delta sigma weight residual 1.473 1.638 -0.165 1.40e-02 5.10e+03 1.39e+02 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 93.05 - 103.11: 129 103.11 - 113.18: 8130 113.18 - 123.24: 10828 123.24 - 133.30: 599 133.30 - 143.36: 20 Bond angle restraints: 19706 Sorted by residual: angle pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" C LEU C 130 " ideal model delta sigma weight residual 113.61 133.76 -20.15 1.50e+00 4.44e-01 1.80e+02 angle pdb=" N THR C 118 " pdb=" CA THR C 118 " pdb=" C THR C 118 " ideal model delta sigma weight residual 111.14 121.30 -10.16 1.08e+00 8.57e-01 8.84e+01 angle pdb=" CG1 VAL C 120 " pdb=" CB VAL C 120 " pdb=" CG2 VAL C 120 " ideal model delta sigma weight residual 110.80 95.30 15.50 2.20e+00 2.07e-01 4.97e+01 angle pdb=" N PRO D 111 " pdb=" CD PRO D 111 " pdb=" CG PRO D 111 " ideal model delta sigma weight residual 103.20 93.05 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 112.00 102.63 9.37 1.40e+00 5.10e-01 4.48e+01 ... (remaining 19701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.40: 8250 18.40 - 36.79: 335 36.79 - 55.19: 55 55.19 - 73.59: 11 73.59 - 91.98: 4 Dihedral angle restraints: 8655 sinusoidal: 3555 harmonic: 5100 Sorted by residual: dihedral pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual 122.80 145.09 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" C LEU C 130 " pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual -122.60 -144.35 21.75 0 2.50e+00 1.60e-01 7.57e+01 dihedral pdb=" CA TYR A 971 " pdb=" C TYR A 971 " pdb=" N GLY A 972 " pdb=" CA GLY A 972 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2202 0.219 - 0.439: 4 0.439 - 0.658: 1 0.658 - 0.877: 1 0.877 - 1.096: 1 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CA LEU C 130 " pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CB LEU C 130 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA PRO D 111 " pdb=" N PRO D 111 " pdb=" C PRO D 111 " pdb=" CB PRO D 111 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.85e+00 ... (remaining 2206 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 117 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ARG C 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG C 117 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 125 " -0.015 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE C 125 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 125 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 125 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 125 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 125 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 116 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C SER C 116 " -0.027 2.00e-02 2.50e+03 pdb=" O SER C 116 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG C 117 " 0.009 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 4 1.61 - 2.44: 47 2.44 - 3.26: 15206 3.26 - 4.08: 34147 4.08 - 4.90: 62723 Warning: very small nonbonded interaction distances. Nonbonded interactions: 112127 Sorted by model distance: nonbonded pdb=" OD1 ASP A1053 " pdb=" NH1 ARG D 117 " model vdw 0.793 2.520 nonbonded pdb=" NH2 ARG A1193 " pdb=" CA VAL D 113 " model vdw 1.528 3.550 nonbonded pdb=" CE2 TYR B 264 " pdb=" N ARG C 117 " model vdw 1.529 3.420 nonbonded pdb=" OD1 ASP A1053 " pdb=" CZ ARG D 117 " model vdw 1.553 3.270 nonbonded pdb=" CE2 TYR B 264 " pdb=" C SER C 116 " model vdw 1.675 3.570 ... (remaining 112122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 4.660 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.430 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.007 0.352 14500 Z= 0.480 Angle : 0.761 20.148 19706 Z= 0.446 Chirality : 0.054 1.096 2209 Planarity : 0.004 0.038 2461 Dihedral : 10.785 91.984 5371 Min Nonbonded Distance : 0.793 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.90 % Favored : 95.87 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % 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: -2.17 (0.19), residues: 1719 helix: -3.31 (0.11), residues: 727 sheet: -1.82 (0.35), residues: 155 loop : 0.78 (0.22), residues: 837 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 456 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 469 average time/residue: 0.3119 time to fit residues: 202.0918 Evaluate side-chains 238 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1282 time to fit residues: 3.2760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 276 ASN A 413 HIS A 519 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN B 436 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 14500 Z= 0.349 Angle : 0.694 10.593 19706 Z= 0.358 Chirality : 0.043 0.166 2209 Planarity : 0.004 0.033 2461 Dihedral : 7.828 89.301 2084 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer Outliers : 4.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1719 helix: -1.26 (0.17), residues: 739 sheet: -1.50 (0.36), residues: 176 loop : 0.39 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 256 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 34 residues processed: 299 average time/residue: 0.2835 time to fit residues: 121.9599 Evaluate side-chains 243 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1424 time to fit residues: 10.7293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14500 Z= 0.184 Angle : 0.579 9.162 19706 Z= 0.294 Chirality : 0.040 0.155 2209 Planarity : 0.003 0.037 2461 Dihedral : 7.419 88.410 2084 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1719 helix: -0.57 (0.18), residues: 744 sheet: -1.13 (0.35), residues: 180 loop : 0.26 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 6 residues processed: 268 average time/residue: 0.2893 time to fit residues: 112.2157 Evaluate side-chains 210 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1380 time to fit residues: 3.6183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.0870 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 188 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14500 Z= 0.175 Angle : 0.571 9.789 19706 Z= 0.286 Chirality : 0.040 0.186 2209 Planarity : 0.003 0.037 2461 Dihedral : 7.058 87.601 2084 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1719 helix: -0.21 (0.19), residues: 745 sheet: -0.85 (0.34), residues: 192 loop : 0.24 (0.23), residues: 782 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 239 average time/residue: 0.2758 time to fit residues: 96.1375 Evaluate side-chains 211 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1322 time to fit residues: 5.7731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 81 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14500 Z= 0.301 Angle : 0.620 9.238 19706 Z= 0.315 Chirality : 0.041 0.186 2209 Planarity : 0.004 0.037 2461 Dihedral : 7.091 87.705 2084 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1719 helix: -0.14 (0.19), residues: 747 sheet: -0.83 (0.34), residues: 194 loop : 0.08 (0.23), residues: 778 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 216 average time/residue: 0.2731 time to fit residues: 87.4037 Evaluate side-chains 190 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 177 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1506 time to fit residues: 6.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 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 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14500 Z= 0.208 Angle : 0.591 10.104 19706 Z= 0.294 Chirality : 0.040 0.177 2209 Planarity : 0.003 0.038 2461 Dihedral : 6.920 86.968 2084 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1719 helix: 0.03 (0.19), residues: 751 sheet: -0.65 (0.35), residues: 193 loop : 0.09 (0.23), residues: 775 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 211 average time/residue: 0.2779 time to fit residues: 86.3073 Evaluate side-chains 204 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1382 time to fit residues: 6.3126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14500 Z= 0.214 Angle : 0.590 9.223 19706 Z= 0.294 Chirality : 0.040 0.180 2209 Planarity : 0.003 0.039 2461 Dihedral : 6.816 87.053 2084 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.92 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1719 helix: 0.19 (0.19), residues: 730 sheet: -0.51 (0.36), residues: 193 loop : 0.14 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 205 average time/residue: 0.2669 time to fit residues: 80.7933 Evaluate side-chains 195 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1455 time to fit residues: 4.6261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 129 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 14500 Z= 0.162 Angle : 0.587 11.721 19706 Z= 0.289 Chirality : 0.039 0.180 2209 Planarity : 0.003 0.040 2461 Dihedral : 6.663 86.602 2084 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1719 helix: 0.29 (0.19), residues: 741 sheet: -0.35 (0.36), residues: 193 loop : 0.15 (0.23), residues: 785 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 206 average time/residue: 0.2743 time to fit residues: 83.8385 Evaluate side-chains 193 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1321 time to fit residues: 2.9178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14500 Z= 0.199 Angle : 0.607 10.741 19706 Z= 0.299 Chirality : 0.040 0.183 2209 Planarity : 0.003 0.039 2461 Dihedral : 6.619 87.088 2084 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.03 % Favored : 96.92 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1719 helix: 0.32 (0.20), residues: 733 sheet: -0.21 (0.37), residues: 191 loop : 0.12 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 203 average time/residue: 0.2842 time to fit residues: 84.5019 Evaluate side-chains 199 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1526 time to fit residues: 4.0888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.0970 chunk 99 optimal weight: 0.2980 chunk 77 optimal weight: 0.4980 chunk 112 optimal weight: 0.2980 chunk 170 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN A 974 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 14500 Z= 0.151 Angle : 0.611 10.834 19706 Z= 0.297 Chirality : 0.039 0.180 2209 Planarity : 0.003 0.041 2461 Dihedral : 6.458 86.377 2084 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1719 helix: 0.30 (0.19), residues: 743 sheet: -0.15 (0.37), residues: 191 loop : 0.16 (0.23), residues: 785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 1.675 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 222 average time/residue: 0.2760 time to fit residues: 89.8525 Evaluate side-chains 199 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1307 time to fit residues: 2.5852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 125 optimal weight: 0.0470 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 ASN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS B 212 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081716 restraints weight = 34547.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084376 restraints weight = 19302.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086194 restraints weight = 12823.876| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 14500 Z= 0.164 Angle : 0.628 12.724 19706 Z= 0.304 Chirality : 0.039 0.182 2209 Planarity : 0.003 0.040 2461 Dihedral : 6.444 86.382 2084 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.96 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1719 helix: 0.30 (0.19), residues: 744 sheet: -0.07 (0.38), residues: 189 loop : 0.16 (0.22), residues: 786 =============================================================================== Job complete usr+sys time: 2849.43 seconds wall clock time: 53 minutes 9.46 seconds (3189.46 seconds total)