Starting phenix.real_space_refine on Fri Mar 15 11:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jy5_36720/03_2024/8jy5_36720.pdb" } resolution = 4.17 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= 0.007 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7448 2.51 5 N 1908 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A TYR 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A ASP 1287": "OD1" <-> "OD2" Residue "A ASP 1293": "OD1" <-> "OD2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1429": "OE1" <-> "OE2" Residue "A GLU 1432": "OE1" <-> "OE2" Residue "A GLU 1462": "OE1" <-> "OE2" Residue "A GLU 1514": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11511 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1457, 11511 Classifications: {'peptide': 1457} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1412} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.76, per 1000 atoms: 0.59 Number of scatterers: 11511 At special positions: 0 Unit cell: (94.16, 123.05, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2097 8.00 N 1908 7.00 C 7448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 2.4 seconds 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 69.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.567A pdb=" N PHE A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.617A pdb=" N GLU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 29' Processing helix chain 'A' and resid 33 through 54 removed outlier: 3.584A pdb=" N LEU A 43 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.700A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 removed outlier: 3.653A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.976A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.901A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 removed outlier: 4.087A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.535A pdb=" N ILE A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.891A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.538A pdb=" N ILE A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.981A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 352 removed outlier: 6.932A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 4.023A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 405 removed outlier: 4.220A pdb=" N GLY A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.672A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.768A pdb=" N MET A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 459 removed outlier: 4.291A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 4.067A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.128A pdb=" N LYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.548A pdb=" N PHE A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 568 removed outlier: 3.597A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Proline residue: A 554 - end of helix removed outlier: 3.549A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 595 removed outlier: 4.126A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 595 through 618 removed outlier: 3.500A pdb=" N MET A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.786A pdb=" N ILE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 721 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 762 through 777 removed outlier: 3.601A pdb=" N GLN A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 824 through 828 Processing helix chain 'A' and resid 844 through 852 removed outlier: 3.567A pdb=" N LYS A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.716A pdb=" N LYS A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.643A pdb=" N ILE A 894 " --> pdb=" O VAL A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 914 removed outlier: 3.581A pdb=" N MET A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 906 " --> pdb=" O THR A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 974 removed outlier: 3.519A pdb=" N ILE A 974 " --> pdb=" O TYR A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.625A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 984 " --> pdb=" O PHE A 980 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1005 " --> pdb=" O SER A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 Processing helix chain 'A' and resid 1022 through 1065 removed outlier: 3.591A pdb=" N GLY A1035 " --> pdb=" O GLY A1031 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A1047 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.522A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1092 removed outlier: 4.086A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A1087 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1120 removed outlier: 4.150A pdb=" N GLN A1097 " --> pdb=" O ASP A1093 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A1100 " --> pdb=" O PRO A1096 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1168 removed outlier: 3.818A pdb=" N ILE A1126 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A1128 " --> pdb=" O THR A1124 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.527A pdb=" N ARG A1146 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A1147 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.573A pdb=" N SER A1168 " --> pdb=" O SER A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 3.602A pdb=" N ALA A1175 " --> pdb=" O PRO A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.541A pdb=" N ASP A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A1197 " --> pdb=" O ASN A1193 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A1202 " --> pdb=" O PHE A1198 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A1203 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A1208 " --> pdb=" O ASN A1204 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A1209 " --> pdb=" O ARG A1205 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A1213 " --> pdb=" O ILE A1209 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1217 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A1222 " --> pdb=" O THR A1218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1224 " --> pdb=" O PHE A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1244 removed outlier: 4.016A pdb=" N PHE A1240 " --> pdb=" O ASP A1236 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1266 removed outlier: 3.738A pdb=" N ASN A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1277 Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.581A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1391 through 1396 Processing helix chain 'A' and resid 1402 through 1413 Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1424 through 1427 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 Processing helix chain 'A' and resid 1468 through 1483 removed outlier: 3.570A pdb=" N ILE A1479 " --> pdb=" O ILE A1475 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1480 " --> pdb=" O GLN A1476 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A1481 " --> pdb=" O THR A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1535 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.784A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 693 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 641 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 695 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 639 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 697 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 637 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA A 642 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.784A pdb=" N SER A 643 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 693 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 641 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 695 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 639 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE A 697 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET A 637 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.755A pdb=" N ASP A 785 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 782 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL A 818 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 784 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 667 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 833 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 714 removed outlier: 4.063A pdb=" N GLY A 713 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1315 through 1320 removed outlier: 5.781A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1315 through 1320 removed outlier: 5.781A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 4.151A pdb=" N ASP A1461 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1389 through 1390 669 hydrogen bonds defined for protein. 1941 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: 4.45 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3650 1.34 - 1.46: 2731 1.46 - 1.58: 5275 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11752 Sorted by residual: bond pdb=" C SER A 339 " pdb=" N PRO A 340 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.45e+00 bond pdb=" C ASN A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.35e+00 bond pdb=" N ASP A 656 " pdb=" CA ASP A 656 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" CA THR A 873 " pdb=" CB THR A 873 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.49e-02 4.50e+03 1.50e+00 bond pdb=" CA PRO A1384 " pdb=" C PRO A1384 " ideal model delta sigma weight residual 1.527 1.514 0.013 1.07e-02 8.73e+03 1.47e+00 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.71: 190 105.71 - 112.82: 6446 112.82 - 119.92: 3906 119.92 - 127.03: 5272 127.03 - 134.14: 126 Bond angle restraints: 15940 Sorted by residual: angle pdb=" C ASP A 22 " pdb=" N LEU A 23 " pdb=" CA LEU A 23 " ideal model delta sigma weight residual 120.65 125.99 -5.34 1.36e+00 5.41e-01 1.54e+01 angle pdb=" C VAL A 229 " pdb=" N ASP A 230 " pdb=" CA ASP A 230 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N SER A 462 " pdb=" CA SER A 462 " pdb=" C SER A 462 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.25e+01 angle pdb=" CA MET A 988 " pdb=" CB MET A 988 " pdb=" CG MET A 988 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C SER A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta sigma weight residual 122.26 116.35 5.91 1.73e+00 3.34e-01 1.17e+01 ... (remaining 15935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 6349 17.82 - 35.64: 542 35.64 - 53.46: 91 53.46 - 71.28: 17 71.28 - 89.10: 8 Dihedral angle restraints: 7007 sinusoidal: 2760 harmonic: 4247 Sorted by residual: dihedral pdb=" CA PHE A 437 " pdb=" C PHE A 437 " pdb=" N MET A 438 " pdb=" CA MET A 438 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 26 " pdb=" CB CYS A 26 " ideal model delta sinusoidal sigma weight residual 93.00 63.78 29.22 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CA ARG A1349 " pdb=" C ARG A1349 " pdb=" N ILE A1350 " pdb=" CA ILE A1350 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 7004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1596 0.056 - 0.112: 241 0.112 - 0.168: 26 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CB ILE A 894 " pdb=" CA ILE A 894 " pdb=" CG1 ILE A 894 " pdb=" CG2 ILE A 894 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA THR A 553 " pdb=" N THR A 553 " pdb=" C THR A 553 " pdb=" CB THR A 553 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CG LEU A1170 " pdb=" CB LEU A1170 " pdb=" CD1 LEU A1170 " pdb=" CD2 LEU A1170 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 1863 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1383 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO A1384 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1384 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1384 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 442 " -0.007 2.00e-02 2.50e+03 1.26e-02 3.97e+00 pdb=" CG TRP A 442 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 442 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 442 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 442 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 442 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 442 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 442 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 442 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 474 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 475 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.022 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 189 2.68 - 3.23: 12561 3.23 - 3.79: 18320 3.79 - 4.34: 24736 4.34 - 4.90: 37678 Nonbonded interactions: 93484 Sorted by model distance: nonbonded pdb=" NE2 GLN A 767 " pdb=" O ASP A 786 " model vdw 2.119 2.520 nonbonded pdb=" OG SER A1234 " pdb=" OD1 ASP A1236 " model vdw 2.194 2.440 nonbonded pdb=" OD2 ASP A 786 " pdb=" OG SER A 789 " model vdw 2.209 2.440 nonbonded pdb=" OH TYR A 209 " pdb=" O SER A1199 " model vdw 2.228 2.440 nonbonded pdb=" ND2 ASN A 409 " pdb=" O GLU A 687 " model vdw 2.235 2.520 ... (remaining 93479 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.003 0.043 11752 Z= 0.175 Angle : 0.656 8.987 15940 Z= 0.361 Chirality : 0.041 0.280 1866 Planarity : 0.004 0.073 1988 Dihedral : 13.663 89.097 4250 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.01 (0.22), residues: 1451 helix: 0.20 (0.17), residues: 874 sheet: 0.74 (0.53), residues: 86 loop : -0.22 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 442 HIS 0.004 0.001 HIS A1496 PHE 0.014 0.001 PHE A 981 TYR 0.015 0.001 TYR A 319 ARG 0.006 0.000 ARG A1257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.9437 (tt) cc_final: 0.9093 (tp) REVERT: A 140 ILE cc_start: 0.9445 (mt) cc_final: 0.9159 (tp) REVERT: A 363 CYS cc_start: 0.8757 (m) cc_final: 0.7965 (t) REVERT: A 446 LEU cc_start: 0.9388 (tp) cc_final: 0.9078 (tp) REVERT: A 450 LEU cc_start: 0.9403 (tt) cc_final: 0.8876 (tp) REVERT: A 559 VAL cc_start: 0.9589 (t) cc_final: 0.9122 (t) REVERT: A 583 ILE cc_start: 0.9379 (pt) cc_final: 0.9174 (pt) REVERT: A 603 MET cc_start: 0.8042 (tmm) cc_final: 0.7820 (tmm) REVERT: A 685 LEU cc_start: 0.9159 (mt) cc_final: 0.8815 (tp) REVERT: A 688 MET cc_start: 0.5618 (tpt) cc_final: 0.5384 (tpp) REVERT: A 887 LEU cc_start: 0.6924 (mt) cc_final: 0.6140 (mt) REVERT: A 905 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8483 (tpt-90) REVERT: A 906 GLU cc_start: 0.9136 (tp30) cc_final: 0.8768 (tm-30) REVERT: A 1116 ILE cc_start: 0.9644 (mt) cc_final: 0.9435 (mt) REVERT: A 1141 TYR cc_start: 0.8218 (t80) cc_final: 0.7968 (t80) REVERT: A 1255 LEU cc_start: 0.9360 (tp) cc_final: 0.9109 (tp) REVERT: A 1273 THR cc_start: 0.9549 (p) cc_final: 0.9124 (p) REVERT: A 1314 ASP cc_start: 0.8851 (m-30) cc_final: 0.8572 (p0) REVERT: A 1327 MET cc_start: 0.6781 (mmp) cc_final: 0.6469 (mmp) REVERT: A 1351 LEU cc_start: 0.9217 (mt) cc_final: 0.8557 (tp) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2266 time to fit residues: 89.9165 Evaluate side-chains 189 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.0030 chunk 84 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11752 Z= 0.196 Angle : 0.648 11.247 15940 Z= 0.336 Chirality : 0.043 0.212 1866 Planarity : 0.004 0.084 1988 Dihedral : 4.223 18.995 1553 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.41 % Favored : 97.52 % Rotamer: Outliers : 0.31 % Allowed : 4.32 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.44 (0.22), residues: 1451 helix: 0.74 (0.17), residues: 895 sheet: 0.43 (0.52), residues: 86 loop : -0.42 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1206 HIS 0.005 0.001 HIS A1496 PHE 0.017 0.002 PHE A 586 TYR 0.013 0.001 TYR A 967 ARG 0.005 0.000 ARG A1083 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8830 (m-80) cc_final: 0.8521 (m-80) REVERT: A 433 ASP cc_start: 0.8830 (m-30) cc_final: 0.8317 (m-30) REVERT: A 603 MET cc_start: 0.7980 (tmm) cc_final: 0.7728 (tmm) REVERT: A 817 LEU cc_start: 0.9301 (tp) cc_final: 0.9001 (pp) REVERT: A 822 MET cc_start: 0.7857 (mtt) cc_final: 0.7339 (mtp) REVERT: A 905 ARG cc_start: 0.8951 (tpt170) cc_final: 0.8451 (tpt-90) REVERT: A 906 GLU cc_start: 0.9127 (tp30) cc_final: 0.8740 (tm-30) REVERT: A 988 MET cc_start: 0.9085 (ppp) cc_final: 0.8376 (ppp) REVERT: A 1034 GLN cc_start: 0.8384 (mm110) cc_final: 0.8133 (mm-40) REVERT: A 1193 ASN cc_start: 0.8747 (t0) cc_final: 0.8426 (t0) REVERT: A 1216 ASN cc_start: 0.8525 (p0) cc_final: 0.7314 (p0) REVERT: A 1225 MET cc_start: 0.8514 (mpp) cc_final: 0.8306 (mtt) REVERT: A 1255 LEU cc_start: 0.9503 (tp) cc_final: 0.9256 (tp) REVERT: A 1273 THR cc_start: 0.9735 (p) cc_final: 0.9381 (p) REVERT: A 1327 MET cc_start: 0.6806 (mmp) cc_final: 0.6489 (mmp) REVERT: A 1351 LEU cc_start: 0.9292 (mt) cc_final: 0.8624 (tp) REVERT: A 1499 MET cc_start: 0.8537 (mtt) cc_final: 0.8221 (mtt) REVERT: A 1505 MET cc_start: 0.8792 (tpt) cc_final: 0.8472 (tpt) outliers start: 4 outliers final: 0 residues processed: 228 average time/residue: 0.1984 time to fit residues: 68.7533 Evaluate side-chains 177 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11752 Z= 0.226 Angle : 0.624 10.493 15940 Z= 0.326 Chirality : 0.042 0.213 1866 Planarity : 0.004 0.037 1988 Dihedral : 4.109 17.088 1553 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.53 (0.22), residues: 1451 helix: 0.85 (0.17), residues: 907 sheet: 0.34 (0.53), residues: 86 loop : -0.48 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1044 HIS 0.004 0.001 HIS A1496 PHE 0.020 0.002 PHE A1106 TYR 0.010 0.001 TYR A1275 ARG 0.004 0.000 ARG A1066 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.9374 (mm) cc_final: 0.9005 (tp) REVERT: A 145 PHE cc_start: 0.8804 (m-80) cc_final: 0.8456 (m-80) REVERT: A 433 ASP cc_start: 0.8961 (m-30) cc_final: 0.8420 (m-30) REVERT: A 603 MET cc_start: 0.8060 (tmm) cc_final: 0.7695 (tmm) REVERT: A 688 MET cc_start: 0.5427 (tpt) cc_final: 0.5191 (tpp) REVERT: A 817 LEU cc_start: 0.9319 (tp) cc_final: 0.9023 (pp) REVERT: A 822 MET cc_start: 0.8065 (mtt) cc_final: 0.7525 (mtp) REVERT: A 905 ARG cc_start: 0.9031 (tpt170) cc_final: 0.8734 (tpt-90) REVERT: A 906 GLU cc_start: 0.9190 (tp30) cc_final: 0.8847 (tm-30) REVERT: A 1193 ASN cc_start: 0.8726 (t0) cc_final: 0.8387 (t0) REVERT: A 1209 ILE cc_start: 0.9152 (tp) cc_final: 0.8740 (tp) REVERT: A 1255 LEU cc_start: 0.9491 (tp) cc_final: 0.9247 (tp) REVERT: A 1273 THR cc_start: 0.9736 (p) cc_final: 0.9464 (p) REVERT: A 1327 MET cc_start: 0.6963 (mmp) cc_final: 0.6637 (mmp) REVERT: A 1351 LEU cc_start: 0.9234 (mt) cc_final: 0.8583 (tp) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2135 time to fit residues: 64.8557 Evaluate side-chains 165 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 GLN A1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11752 Z= 0.336 Angle : 0.697 7.092 15940 Z= 0.374 Chirality : 0.043 0.212 1866 Planarity : 0.004 0.037 1988 Dihedral : 4.456 21.921 1553 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.33 (0.21), residues: 1451 helix: 0.68 (0.16), residues: 914 sheet: 0.25 (0.54), residues: 89 loop : -0.55 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.048 0.002 PHE A1037 TYR 0.018 0.002 TYR A 616 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 187 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8614 (m-80) cc_final: 0.8344 (m-80) REVERT: A 145 PHE cc_start: 0.8864 (m-80) cc_final: 0.8434 (m-80) REVERT: A 432 MET cc_start: 0.8510 (mmp) cc_final: 0.8233 (mmp) REVERT: A 433 ASP cc_start: 0.8967 (m-30) cc_final: 0.8639 (m-30) REVERT: A 603 MET cc_start: 0.8237 (tmm) cc_final: 0.7921 (tmm) REVERT: A 688 MET cc_start: 0.6466 (tpt) cc_final: 0.6187 (tpp) REVERT: A 817 LEU cc_start: 0.9350 (tp) cc_final: 0.9059 (pp) REVERT: A 822 MET cc_start: 0.8266 (mtt) cc_final: 0.7766 (mtt) REVERT: A 905 ARG cc_start: 0.9007 (tpt170) cc_final: 0.8702 (tpt-90) REVERT: A 906 GLU cc_start: 0.9225 (tp30) cc_final: 0.8873 (tm-30) REVERT: A 1037 PHE cc_start: 0.8822 (m-80) cc_final: 0.8485 (m-80) REVERT: A 1064 ILE cc_start: 0.8462 (pt) cc_final: 0.8160 (pt) REVERT: A 1123 PHE cc_start: 0.8702 (t80) cc_final: 0.8223 (t80) REVERT: A 1249 THR cc_start: 0.8733 (p) cc_final: 0.8341 (p) REVERT: A 1255 LEU cc_start: 0.9514 (tp) cc_final: 0.9266 (tp) REVERT: A 1351 LEU cc_start: 0.9198 (mt) cc_final: 0.8460 (tp) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1965 time to fit residues: 55.9129 Evaluate side-chains 148 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11752 Z= 0.182 Angle : 0.619 7.506 15940 Z= 0.314 Chirality : 0.042 0.211 1866 Planarity : 0.004 0.082 1988 Dihedral : 4.273 19.798 1553 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.59 (0.22), residues: 1451 helix: 0.95 (0.17), residues: 917 sheet: 0.11 (0.52), residues: 91 loop : -0.57 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.028 0.002 PHE A 586 TYR 0.013 0.001 TYR A1275 ARG 0.009 0.001 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ILE cc_start: 0.9344 (mm) cc_final: 0.9027 (tp) REVERT: A 145 PHE cc_start: 0.8779 (m-80) cc_final: 0.8327 (m-80) REVERT: A 363 CYS cc_start: 0.8715 (m) cc_final: 0.8330 (t) REVERT: A 433 ASP cc_start: 0.8726 (m-30) cc_final: 0.8524 (m-30) REVERT: A 603 MET cc_start: 0.8185 (tmm) cc_final: 0.7856 (tmm) REVERT: A 822 MET cc_start: 0.7974 (mtt) cc_final: 0.7531 (mtp) REVERT: A 906 GLU cc_start: 0.9239 (tp30) cc_final: 0.8865 (tm-30) REVERT: A 1193 ASN cc_start: 0.8740 (t0) cc_final: 0.8233 (t0) REVERT: A 1254 TRP cc_start: 0.7161 (t-100) cc_final: 0.6882 (t-100) REVERT: A 1255 LEU cc_start: 0.9421 (tp) cc_final: 0.9163 (tp) REVERT: A 1258 MET cc_start: 0.7609 (ptp) cc_final: 0.7353 (ptp) REVERT: A 1351 LEU cc_start: 0.9156 (mt) cc_final: 0.8407 (tp) REVERT: A 1505 MET cc_start: 0.8769 (mmp) cc_final: 0.8212 (tpp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1978 time to fit residues: 62.4336 Evaluate side-chains 163 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11752 Z= 0.250 Angle : 0.633 7.437 15940 Z= 0.329 Chirality : 0.041 0.201 1866 Planarity : 0.004 0.063 1988 Dihedral : 4.277 18.974 1553 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.51 (0.22), residues: 1451 helix: 0.91 (0.17), residues: 917 sheet: 0.06 (0.57), residues: 80 loop : -0.65 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.017 0.001 PHE A 135 TYR 0.012 0.001 TYR A 885 ARG 0.005 0.001 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.8284 (m100) cc_final: 0.7866 (m100) REVERT: A 140 ILE cc_start: 0.9374 (mm) cc_final: 0.9073 (tp) REVERT: A 145 PHE cc_start: 0.8815 (m-80) cc_final: 0.8365 (m-80) REVERT: A 603 MET cc_start: 0.8279 (tmm) cc_final: 0.7967 (tmm) REVERT: A 822 MET cc_start: 0.7975 (mtt) cc_final: 0.7570 (mtp) REVERT: A 906 GLU cc_start: 0.9267 (tp30) cc_final: 0.8898 (tm-30) REVERT: A 1255 LEU cc_start: 0.9438 (tp) cc_final: 0.9185 (tp) REVERT: A 1351 LEU cc_start: 0.9160 (mt) cc_final: 0.8425 (tp) REVERT: A 1505 MET cc_start: 0.8845 (mmp) cc_final: 0.8293 (tpp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2139 time to fit residues: 61.9415 Evaluate side-chains 152 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11752 Z= 0.207 Angle : 0.610 6.892 15940 Z= 0.315 Chirality : 0.041 0.201 1866 Planarity : 0.004 0.047 1988 Dihedral : 4.229 18.456 1553 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.57 (0.22), residues: 1451 helix: 0.96 (0.17), residues: 918 sheet: -0.06 (0.57), residues: 80 loop : -0.59 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.024 0.001 PHE A 74 TYR 0.010 0.001 TYR A 107 ARG 0.004 0.000 ARG A 729 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.8243 (m100) cc_final: 0.7771 (m100) REVERT: A 140 ILE cc_start: 0.9355 (mm) cc_final: 0.9067 (tp) REVERT: A 145 PHE cc_start: 0.8817 (m-80) cc_final: 0.8353 (m-80) REVERT: A 603 MET cc_start: 0.8243 (tmm) cc_final: 0.7942 (tmm) REVERT: A 822 MET cc_start: 0.8137 (mtt) cc_final: 0.7782 (mtp) REVERT: A 906 GLU cc_start: 0.9273 (tp30) cc_final: 0.8875 (tm-30) REVERT: A 1193 ASN cc_start: 0.8722 (t0) cc_final: 0.8184 (t0) REVERT: A 1249 THR cc_start: 0.8748 (p) cc_final: 0.8265 (p) REVERT: A 1351 LEU cc_start: 0.9110 (mt) cc_final: 0.8447 (tp) REVERT: A 1505 MET cc_start: 0.8849 (mmp) cc_final: 0.8304 (tpp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1946 time to fit residues: 57.0071 Evaluate side-chains 147 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 127 optimal weight: 40.0000 chunk 133 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11752 Z= 0.196 Angle : 0.633 10.656 15940 Z= 0.319 Chirality : 0.042 0.229 1866 Planarity : 0.004 0.044 1988 Dihedral : 4.202 18.872 1553 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.61 (0.22), residues: 1451 helix: 0.98 (0.17), residues: 919 sheet: -0.13 (0.56), residues: 81 loop : -0.55 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1044 HIS 0.005 0.001 HIS A1496 PHE 0.016 0.001 PHE A1037 TYR 0.018 0.001 TYR A1275 ARG 0.006 0.001 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.8393 (mm) cc_final: 0.8185 (mm) REVERT: A 136 TRP cc_start: 0.8172 (m100) cc_final: 0.7745 (m100) REVERT: A 140 ILE cc_start: 0.9352 (mm) cc_final: 0.9062 (tp) REVERT: A 145 PHE cc_start: 0.8815 (m-80) cc_final: 0.8355 (m-80) REVERT: A 603 MET cc_start: 0.8243 (tmm) cc_final: 0.7944 (tmm) REVERT: A 822 MET cc_start: 0.8155 (mtt) cc_final: 0.7834 (mtp) REVERT: A 906 GLU cc_start: 0.9278 (tp30) cc_final: 0.8864 (tm-30) REVERT: A 1193 ASN cc_start: 0.8688 (t0) cc_final: 0.8155 (t0) REVERT: A 1351 LEU cc_start: 0.9078 (mt) cc_final: 0.8436 (tp) REVERT: A 1505 MET cc_start: 0.8857 (mmp) cc_final: 0.8276 (tpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2031 time to fit residues: 59.3347 Evaluate side-chains 147 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11752 Z= 0.222 Angle : 0.644 9.812 15940 Z= 0.326 Chirality : 0.042 0.195 1866 Planarity : 0.004 0.042 1988 Dihedral : 4.240 19.276 1553 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.54 (0.22), residues: 1451 helix: 0.92 (0.17), residues: 920 sheet: -0.24 (0.57), residues: 80 loop : -0.53 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1206 HIS 0.005 0.001 HIS A1496 PHE 0.020 0.001 PHE A1037 TYR 0.024 0.001 TYR A1275 ARG 0.005 0.001 ARG A1174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.9295 (p) cc_final: 0.8663 (m) REVERT: A 136 TRP cc_start: 0.8284 (m100) cc_final: 0.7997 (m100) REVERT: A 145 PHE cc_start: 0.8847 (m-80) cc_final: 0.8369 (m-80) REVERT: A 433 ASP cc_start: 0.8699 (m-30) cc_final: 0.8361 (m-30) REVERT: A 583 ILE cc_start: 0.9498 (pt) cc_final: 0.8977 (pt) REVERT: A 603 MET cc_start: 0.8397 (tmm) cc_final: 0.8071 (tmm) REVERT: A 822 MET cc_start: 0.8235 (mtt) cc_final: 0.7912 (mtp) REVERT: A 906 GLU cc_start: 0.9253 (tp30) cc_final: 0.8827 (tm-30) REVERT: A 1064 ILE cc_start: 0.8219 (pt) cc_final: 0.7937 (pt) REVERT: A 1193 ASN cc_start: 0.8709 (t0) cc_final: 0.8175 (t0) REVERT: A 1246 LEU cc_start: 0.9374 (mm) cc_final: 0.9162 (pp) REVERT: A 1249 THR cc_start: 0.8689 (p) cc_final: 0.8185 (p) REVERT: A 1351 LEU cc_start: 0.9100 (mt) cc_final: 0.8432 (tp) REVERT: A 1505 MET cc_start: 0.8926 (mmp) cc_final: 0.8232 (tpt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2033 time to fit residues: 57.7735 Evaluate side-chains 147 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 11 optimal weight: 0.0060 chunk 88 optimal weight: 0.3980 chunk 70 optimal weight: 30.0000 chunk 91 optimal weight: 0.5980 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11752 Z= 0.170 Angle : 0.638 11.772 15940 Z= 0.314 Chirality : 0.042 0.199 1866 Planarity : 0.004 0.039 1988 Dihedral : 4.214 22.722 1553 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.63 (0.22), residues: 1451 helix: 1.00 (0.17), residues: 919 sheet: -0.19 (0.56), residues: 81 loop : -0.52 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1044 HIS 0.004 0.001 HIS A1496 PHE 0.053 0.001 PHE A1037 TYR 0.023 0.001 TYR A1275 ARG 0.005 0.001 ARG A1174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.9255 (p) cc_final: 0.8559 (m) REVERT: A 145 PHE cc_start: 0.8820 (m-80) cc_final: 0.8339 (m-80) REVERT: A 433 ASP cc_start: 0.8625 (m-30) cc_final: 0.8245 (m-30) REVERT: A 822 MET cc_start: 0.8240 (mtt) cc_final: 0.7958 (mtp) REVERT: A 906 GLU cc_start: 0.9249 (tp30) cc_final: 0.8812 (tm-30) REVERT: A 1069 MET cc_start: 0.9383 (pmm) cc_final: 0.9171 (pmm) REVERT: A 1193 ASN cc_start: 0.8692 (t0) cc_final: 0.8186 (t0) REVERT: A 1254 TRP cc_start: 0.7335 (t-100) cc_final: 0.6757 (t-100) REVERT: A 1255 LEU cc_start: 0.9484 (tp) cc_final: 0.9279 (tp) REVERT: A 1351 LEU cc_start: 0.9074 (mt) cc_final: 0.8402 (tp) REVERT: A 1505 MET cc_start: 0.8984 (mmp) cc_final: 0.8252 (tpt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1949 time to fit residues: 56.3748 Evaluate side-chains 150 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 0.0040 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.033190 restraints weight = 99899.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034184 restraints weight = 69312.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034922 restraints weight = 53394.129| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11752 Z= 0.188 Angle : 0.629 10.485 15940 Z= 0.312 Chirality : 0.042 0.189 1866 Planarity : 0.004 0.038 1988 Dihedral : 4.179 19.765 1553 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.62 (0.22), residues: 1451 helix: 0.98 (0.17), residues: 920 sheet: -0.36 (0.56), residues: 83 loop : -0.45 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1044 HIS 0.004 0.001 HIS A1496 PHE 0.024 0.001 PHE A 586 TYR 0.022 0.001 TYR A1275 ARG 0.004 0.000 ARG A1174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.48 seconds wall clock time: 42 minutes 49.94 seconds (2569.94 seconds total)