Starting phenix.real_space_refine on Sat Dec 9 06:50:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y6k_10706/12_2023/6y6k_10706.pdb" } resolution = 3.78 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= 0.001 sd= 0.013 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 Mg 1 5.21 5 S 63 5.16 5 C 6577 2.51 5 N 1786 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 660": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1169": "OE1" <-> "OE2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A GLU 1184": "OE1" <-> "OE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ASP 1270": "OD1" <-> "OD2" Residue "A GLU 1479": "OE1" <-> "OE2" Residue "A GLU 1492": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10351 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1300, 10351 Unusual residues: {' MG': 1} Classifications: {'peptide': 1299, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1248, None: 1} Not linked: pdbres="GLU A1612 " pdbres=" MG A2101 " Chain breaks: 7 Time building chain proxies: 5.78, per 1000 atoms: 0.56 Number of scatterers: 10351 At special positions: 0 Unit cell: (103.53, 98.31, 113.1, 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 63 16.00 Mg 1 11.99 O 1924 8.00 N 1786 7.00 C 6577 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: 3.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 13 sheets defined 43.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.662A pdb=" N ASP A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.503A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 158 removed outlier: 3.858A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 184 through 207 removed outlier: 3.500A pdb=" N ALA A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.990A pdb=" N GLU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.539A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.117A pdb=" N GLY A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.713A pdb=" N GLU A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 removed outlier: 4.338A pdb=" N LYS A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 318 removed outlier: 3.730A pdb=" N LEU A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.507A pdb=" N CYS A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.722A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 removed outlier: 4.216A pdb=" N LEU A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 removed outlier: 3.750A pdb=" N HIS A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.659A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 521 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 524 " --> pdb=" O TRP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 627 removed outlier: 3.662A pdb=" N THR A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 617 " --> pdb=" O PRO A 613 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 618 " --> pdb=" O CYS A 614 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 627 " --> pdb=" O TRP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 3.766A pdb=" N PHE A 649 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 682 through 687 removed outlier: 4.111A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.504A pdb=" N ARG A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 710 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.530A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 781 removed outlier: 4.402A pdb=" N GLU A 779 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 780 " --> pdb=" O MET A 777 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A 781 " --> pdb=" O GLU A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 781' Processing helix chain 'A' and resid 802 through 807 removed outlier: 3.674A pdb=" N LEU A 806 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 4.248A pdb=" N GLU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 874 through 877 Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.917A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 945 removed outlier: 3.907A pdb=" N LEU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 938 " --> pdb=" O PHE A 934 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 961 removed outlier: 4.124A pdb=" N SER A 960 " --> pdb=" O ARG A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.700A pdb=" N LYS A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.798A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1038 removed outlier: 3.501A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1056 removed outlier: 3.826A pdb=" N ASP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.607A pdb=" N HIS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1092 " --> pdb=" O SER A1088 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A1097 " --> pdb=" O CYS A1093 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1153 removed outlier: 3.633A pdb=" N PHE A1147 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A1148 " --> pdb=" O ARG A1144 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 removed outlier: 3.543A pdb=" N ASN A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1195 through 1201 removed outlier: 3.515A pdb=" N ILE A1199 " --> pdb=" O THR A1195 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1195 through 1201' Processing helix chain 'A' and resid 1214 through 1219 Processing helix chain 'A' and resid 1222 through 1228 Processing helix chain 'A' and resid 1233 through 1238 removed outlier: 3.754A pdb=" N LEU A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1248 removed outlier: 3.591A pdb=" N GLN A1242 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1244 " --> pdb=" O CYS A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1266 removed outlier: 3.790A pdb=" N LEU A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1296 removed outlier: 3.839A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1404 through 1411 removed outlier: 3.540A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.816A pdb=" N ARG A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1479 removed outlier: 3.612A pdb=" N VAL A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A1479 " --> pdb=" O CYS A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.108A pdb=" N GLY A 15 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE A 167 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 17 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 123 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS A 115 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 125 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 6.776A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.797A pdb=" N LYS A 544 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AA7, first strand: chain 'A' and resid 909 through 912 Processing sheet with id=AA8, first strand: chain 'A' and resid 978 through 979 removed outlier: 3.510A pdb=" N ILE A1134 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 981 through 982 removed outlier: 5.798A pdb=" N ASN A 981 " --> pdb=" O ASN A1174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1024 through 1026 removed outlier: 3.896A pdb=" N THR A1074 " --> pdb=" O LYS A1024 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1487 removed outlier: 3.802A pdb=" N LYS A1487 " --> pdb=" O SER A1610 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A1610 " --> pdb=" O LYS A1487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1496 through 1500 removed outlier: 3.835A pdb=" N SER A1498 " --> pdb=" O LEU A1583 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 741 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: 3.45 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2709 1.33 - 1.45: 1930 1.45 - 1.57: 5827 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 10568 Sorted by residual: bond pdb=" C MET A 181 " pdb=" N PRO A 182 " ideal model delta sigma weight residual 1.332 1.387 -0.056 1.32e-02 5.74e+03 1.78e+01 bond pdb=" N PRO A 182 " pdb=" CD PRO A 182 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB ASN A 981 " pdb=" CG ASN A 981 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.80e+00 bond pdb=" CA LEU A 214 " pdb=" C LEU A 214 " ideal model delta sigma weight residual 1.530 1.501 0.028 1.10e-02 8.26e+03 6.63e+00 bond pdb=" CB GLU A1123 " pdb=" CG GLU A1123 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.44e+00 ... (remaining 10563 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.87: 212 105.87 - 114.06: 6151 114.06 - 122.24: 6325 122.24 - 130.42: 1525 130.42 - 138.60: 59 Bond angle restraints: 14272 Sorted by residual: angle pdb=" N TYR A 861 " pdb=" CA TYR A 861 " pdb=" C TYR A 861 " ideal model delta sigma weight residual 111.36 123.61 -12.25 1.09e+00 8.42e-01 1.26e+02 angle pdb=" N ASN A 984 " pdb=" CA ASN A 984 " pdb=" C ASN A 984 " ideal model delta sigma weight residual 110.17 121.98 -11.81 1.51e+00 4.39e-01 6.12e+01 angle pdb=" N LEU A 957 " pdb=" CA LEU A 957 " pdb=" C LEU A 957 " ideal model delta sigma weight residual 111.28 119.08 -7.80 1.09e+00 8.42e-01 5.12e+01 angle pdb=" C MET A 181 " pdb=" N PRO A 182 " pdb=" CA PRO A 182 " ideal model delta sigma weight residual 119.76 113.93 5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" N ALA A 590 " pdb=" CA ALA A 590 " pdb=" C ALA A 590 " ideal model delta sigma weight residual 109.52 100.69 8.83 1.55e+00 4.16e-01 3.24e+01 ... (remaining 14267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5527 17.49 - 34.99: 662 34.99 - 52.48: 146 52.48 - 69.98: 29 69.98 - 87.47: 12 Dihedral angle restraints: 6376 sinusoidal: 2607 harmonic: 3769 Sorted by residual: dihedral pdb=" CA THR A 995 " pdb=" C THR A 995 " pdb=" N THR A 996 " pdb=" CA THR A 996 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLY A 688 " pdb=" C GLY A 688 " pdb=" N LYS A 689 " pdb=" CA LYS A 689 " ideal model delta harmonic sigma weight residual 180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER A 639 " pdb=" C SER A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1376 0.083 - 0.165: 183 0.165 - 0.248: 22 0.248 - 0.330: 3 0.330 - 0.413: 1 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA TYR A 861 " pdb=" N TYR A 861 " pdb=" C TYR A 861 " pdb=" CB TYR A 861 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA ASN A 984 " pdb=" N ASN A 984 " pdb=" C ASN A 984 " pdb=" CB ASN A 984 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA MET A 208 " pdb=" N MET A 208 " pdb=" C MET A 208 " pdb=" CB MET A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1582 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 676 " 0.049 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO A 677 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 30 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 31 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A1006 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO A1007 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1007 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1007 " -0.035 5.00e-02 4.00e+02 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.09: 7482 3.09 - 3.70: 13385 3.70 - 4.30: 19160 4.30 - 4.90: 33074 Nonbonded interactions: 73166 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 1.889 2.170 nonbonded pdb=" N ASN A 954 " pdb=" OD1 ASN A 954 " model vdw 2.159 2.520 nonbonded pdb=" OD1 ASN A 742 " pdb=" ND2 ASN A 745 " model vdw 2.240 2.520 nonbonded pdb=" N ASN A 990 " pdb=" OD1 ASN A 990 " model vdw 2.252 2.520 nonbonded pdb=" OD1 ASP A 209 " pdb=" N ASP A 211 " model vdw 2.256 2.520 ... (remaining 73161 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: 0.420 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: 2.360 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.012 0.089 10568 Z= 0.766 Angle : 0.992 13.604 14272 Z= 0.588 Chirality : 0.060 0.413 1585 Planarity : 0.006 0.073 1821 Dihedral : 15.997 87.472 3936 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.47 % Favored : 87.37 % Rotamer: Outliers : 2.36 % Allowed : 20.30 % Favored : 77.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.16), residues: 1283 helix: -4.20 (0.13), residues: 518 sheet: -2.02 (0.41), residues: 134 loop : -3.85 (0.18), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 520 HIS 0.008 0.002 HIS A1246 PHE 0.026 0.003 PHE A1010 TYR 0.022 0.003 TYR A1110 ARG 0.003 0.001 ARG A1295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.170 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 0.2523 time to fit residues: 51.2645 Evaluate side-chains 115 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.363 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1321 time to fit residues: 5.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 185 GLN A 247 ASN A 500 HIS A 516 GLN A 618 ASN A 644 GLN A 670 GLN A 734 HIS A 799 HIS A 853 ASN A 870 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 HIS A1239 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10568 Z= 0.183 Angle : 0.599 8.252 14272 Z= 0.317 Chirality : 0.043 0.143 1585 Planarity : 0.005 0.064 1821 Dihedral : 5.149 23.104 1407 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 3.06 % Allowed : 21.52 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.19), residues: 1283 helix: -3.24 (0.16), residues: 579 sheet: -0.81 (0.44), residues: 125 loop : -3.51 (0.20), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1294 HIS 0.005 0.001 HIS A 870 PHE 0.012 0.001 PHE A 911 TYR 0.010 0.001 TYR A1110 ARG 0.004 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.223 Fit side-chains outliers start: 35 outliers final: 13 residues processed: 141 average time/residue: 0.2235 time to fit residues: 45.1572 Evaluate side-chains 111 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0951 time to fit residues: 3.9606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.0270 chunk 127 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 HIS A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10568 Z= 0.280 Angle : 0.603 8.212 14272 Z= 0.316 Chirality : 0.044 0.214 1585 Planarity : 0.004 0.058 1821 Dihedral : 4.990 23.127 1407 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 2.10 % Allowed : 23.53 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.20), residues: 1283 helix: -2.76 (0.18), residues: 585 sheet: -0.61 (0.44), residues: 127 loop : -3.43 (0.21), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1294 HIS 0.005 0.001 HIS A1190 PHE 0.016 0.001 PHE A 911 TYR 0.012 0.001 TYR A1110 ARG 0.004 0.000 ARG A1582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.201 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.2113 time to fit residues: 37.5645 Evaluate side-chains 109 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1011 time to fit residues: 4.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 61 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 HIS A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10568 Z= 0.252 Angle : 0.576 7.383 14272 Z= 0.304 Chirality : 0.043 0.139 1585 Planarity : 0.004 0.054 1821 Dihedral : 4.847 22.587 1407 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 1.31 % Allowed : 24.15 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.20), residues: 1283 helix: -2.41 (0.19), residues: 580 sheet: -0.43 (0.45), residues: 125 loop : -3.27 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1294 HIS 0.004 0.001 HIS A1190 PHE 0.016 0.001 PHE A 911 TYR 0.011 0.001 TYR A1110 ARG 0.004 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.130 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 0.2238 time to fit residues: 37.7975 Evaluate side-chains 105 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1393 time to fit residues: 3.1310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0060 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.0010 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 799 HIS A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10568 Z= 0.233 Angle : 0.555 6.615 14272 Z= 0.292 Chirality : 0.042 0.137 1585 Planarity : 0.004 0.053 1821 Dihedral : 4.731 23.013 1407 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.17 % Favored : 92.75 % Rotamer: Outliers : 2.10 % Allowed : 25.02 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.20), residues: 1283 helix: -2.17 (0.20), residues: 580 sheet: -0.25 (0.46), residues: 125 loop : -3.17 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1294 HIS 0.004 0.001 HIS A 447 PHE 0.015 0.001 PHE A 911 TYR 0.011 0.001 TYR A1110 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.412 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 120 average time/residue: 0.2386 time to fit residues: 41.0264 Evaluate side-chains 106 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1066 time to fit residues: 4.0334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS A 895 GLN A1095 GLN A1483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 10568 Z= 0.139 Angle : 0.507 6.306 14272 Z= 0.262 Chirality : 0.040 0.135 1585 Planarity : 0.004 0.051 1821 Dihedral : 4.277 20.261 1407 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.70 % Allowed : 25.72 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.21), residues: 1283 helix: -1.76 (0.20), residues: 578 sheet: 0.04 (0.46), residues: 125 loop : -3.05 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1294 HIS 0.003 0.000 HIS A 447 PHE 0.012 0.001 PHE A 911 TYR 0.015 0.001 TYR A1471 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.211 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 119 average time/residue: 0.2179 time to fit residues: 37.8685 Evaluate side-chains 99 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1122 time to fit residues: 1.9616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 10568 Z= 0.210 Angle : 0.544 10.260 14272 Z= 0.283 Chirality : 0.042 0.237 1585 Planarity : 0.005 0.114 1821 Dihedral : 4.399 20.940 1407 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.96 % Allowed : 26.68 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.21), residues: 1283 helix: -1.65 (0.20), residues: 578 sheet: 0.05 (0.45), residues: 127 loop : -2.94 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.004 0.001 HIS A 447 PHE 0.015 0.001 PHE A 911 TYR 0.010 0.001 TYR A1110 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.302 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 106 average time/residue: 0.2197 time to fit residues: 34.5932 Evaluate side-chains 103 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1355 time to fit residues: 3.1434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 98 optimal weight: 0.0670 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 895 GLN A 933 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.135 10568 Z= 0.144 Angle : 0.504 7.707 14272 Z= 0.259 Chirality : 0.040 0.220 1585 Planarity : 0.004 0.081 1821 Dihedral : 4.062 19.179 1407 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.61 % Allowed : 26.51 % Favored : 72.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1283 helix: -1.23 (0.21), residues: 576 sheet: 0.25 (0.45), residues: 127 loop : -2.86 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1064 HIS 0.004 0.001 HIS A 447 PHE 0.014 0.001 PHE A 911 TYR 0.014 0.001 TYR A 202 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.118 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.2045 time to fit residues: 36.0687 Evaluate side-chains 107 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0978 time to fit residues: 2.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 0.0050 chunk 70 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 0.0270 chunk 35 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 overall best weight: 2.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 10568 Z= 0.212 Angle : 0.551 10.346 14272 Z= 0.284 Chirality : 0.042 0.201 1585 Planarity : 0.004 0.067 1821 Dihedral : 4.223 21.780 1407 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.52 % Allowed : 26.42 % Favored : 73.05 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1283 helix: -1.23 (0.21), residues: 579 sheet: 0.17 (0.44), residues: 129 loop : -2.85 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1064 HIS 0.005 0.001 HIS A 993 PHE 0.016 0.001 PHE A 911 TYR 0.010 0.001 TYR A1110 ARG 0.004 0.000 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.305 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.2227 time to fit residues: 34.1949 Evaluate side-chains 100 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1129 time to fit residues: 2.2084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.2980 chunk 85 optimal weight: 0.0370 chunk 129 optimal weight: 0.4980 chunk 119 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 10568 Z= 0.155 Angle : 0.522 9.121 14272 Z= 0.268 Chirality : 0.040 0.197 1585 Planarity : 0.004 0.053 1821 Dihedral : 4.045 21.083 1407 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.09 % Allowed : 26.86 % Favored : 73.05 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1283 helix: -0.96 (0.21), residues: 580 sheet: 0.34 (0.45), residues: 127 loop : -2.79 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1064 HIS 0.004 0.001 HIS A 447 PHE 0.011 0.001 PHE A 911 TYR 0.013 0.001 TYR A 202 ARG 0.007 0.000 ARG A 823 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.128 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2101 time to fit residues: 33.0174 Evaluate side-chains 100 residues out of total 1143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS A 895 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114122 restraints weight = 13838.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.112510 restraints weight = 26321.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113338 restraints weight = 26646.260| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 10568 Z= 0.230 Angle : 0.556 7.781 14272 Z= 0.288 Chirality : 0.043 0.190 1585 Planarity : 0.004 0.051 1821 Dihedral : 4.291 25.516 1407 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.17 % Allowed : 26.77 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.22), residues: 1283 helix: -1.02 (0.21), residues: 579 sheet: 0.14 (0.44), residues: 129 loop : -2.81 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1064 HIS 0.005 0.001 HIS A1091 PHE 0.015 0.001 PHE A 911 TYR 0.011 0.001 TYR A1110 ARG 0.004 0.000 ARG A 956 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.78 seconds wall clock time: 35 minutes 48.68 seconds (2148.68 seconds total)