Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 02:22:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh6_11215/04_2023/6zh6_11215.pdb" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 192 5.16 5 C 18734 2.51 5 N 4951 2.21 5 O 5324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 29201 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 29138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3692, 29138 Classifications: {'peptide': 3692} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'CIS': 1, 'PTRANS': 160, 'TRANS': 3530} Chain breaks: 18 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 537 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'UNK:plan-1': 27, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 240 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 63 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 15.02, per 1000 atoms: 0.51 Number of scatterers: 29201 At special positions: 0 Unit cell: (124.136, 148.332, 183.048, 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 192 16.00 O 5324 8.00 N 4951 7.00 C 18734 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: 11.80 Conformation dependent library (CDL) restraints added in 4.2 seconds 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7106 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 4 sheets defined 69.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.038A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 73 removed outlier: 4.330A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 96 removed outlier: 3.680A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.012A pdb=" N ASN A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.524A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 172 through 185 removed outlier: 4.487A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.520A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.510A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.845A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.548A pdb=" N PHE A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A 283 " --> pdb=" O SER A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 307 through 324 removed outlier: 3.612A pdb=" N ALA A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.071A pdb=" N TYR A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.908A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.502A pdb=" N ASN A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.548A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 removed outlier: 3.843A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.619A pdb=" N LEU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 removed outlier: 4.055A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.056A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.882A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 removed outlier: 3.846A pdb=" N ILE A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.561A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.241A pdb=" N PHE A 641 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 660 removed outlier: 3.813A pdb=" N GLU A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 678 removed outlier: 4.533A pdb=" N TYR A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 698 through 718 removed outlier: 4.955A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.518A pdb=" N ILE A 741 " --> pdb=" O PRO A 737 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.532A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.736A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.587A pdb=" N ILE A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.142A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 removed outlier: 3.651A pdb=" N VAL A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.322A pdb=" N LYS A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 877 removed outlier: 3.714A pdb=" N SER A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 removed outlier: 4.530A pdb=" N ARG A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 948 removed outlier: 3.550A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 947 " --> pdb=" O GLY A 943 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N MET A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.957A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 972 removed outlier: 3.812A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 996 removed outlier: 3.556A pdb=" N LEU A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) Proline residue: A 986 - end of helix removed outlier: 3.667A pdb=" N MET A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 4.046A pdb=" N THR A1006 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.583A pdb=" N ALA A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'A' and resid 1022 through 1043 removed outlier: 3.693A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 4.297A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1069 removed outlier: 4.110A pdb=" N LYS A1061 " --> pdb=" O LYS A1057 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1062 " --> pdb=" O SER A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1086 removed outlier: 3.619A pdb=" N ASN A1083 " --> pdb=" O SER A1079 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 4.650A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1109 " --> pdb=" O VAL A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 removed outlier: 3.584A pdb=" N CYS A1127 " --> pdb=" O THR A1123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.673A pdb=" N ALA A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1193 removed outlier: 3.816A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1198 Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1217 through 1226 Processing helix chain 'A' and resid 1251 through 1273 removed outlier: 3.581A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.637A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1323 through 1349 removed outlier: 3.687A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1339 " --> pdb=" O CYS A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1358 removed outlier: 3.822A pdb=" N LEU A1358 " --> pdb=" O GLU A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1363 removed outlier: 3.850A pdb=" N ASP A1362 " --> pdb=" O LEU A1359 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A1363 " --> pdb=" O LYS A1360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1359 through 1363' Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.068A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A1371 " --> pdb=" O HIS A1367 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A1374 " --> pdb=" O ARG A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1390 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.553A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A1404 " --> pdb=" O VAL A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.637A pdb=" N THR A1417 " --> pdb=" O ASP A1413 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1434 Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 4.203A pdb=" N ARG A1445 " --> pdb=" O ALA A1441 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A1446 " --> pdb=" O GLN A1442 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A1457 " --> pdb=" O SER A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1486 removed outlier: 4.288A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1492 removed outlier: 3.800A pdb=" N ILE A1491 " --> pdb=" O VAL A1487 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A1492 " --> pdb=" O TYR A1488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1487 through 1492' Processing helix chain 'A' and resid 1506 through 1521 removed outlier: 3.676A pdb=" N PHE A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.649A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.606A pdb=" N LEU A1562 " --> pdb=" O TYR A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1574 removed outlier: 3.730A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 3.793A pdb=" N ALA A1578 " --> pdb=" O ASN A1574 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 removed outlier: 3.691A pdb=" N LEU A1601 " --> pdb=" O LEU A1597 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP A1602 " --> pdb=" O ASN A1598 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1625 removed outlier: 3.673A pdb=" N LEU A1618 " --> pdb=" O GLN A1614 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A1622 " --> pdb=" O LEU A1618 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1623 " --> pdb=" O ALA A1619 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1632 removed outlier: 3.926A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1655 removed outlier: 4.504A pdb=" N ALA A1644 " --> pdb=" O GLU A1640 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1645 " --> pdb=" O THR A1641 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A1646 " --> pdb=" O LYS A1642 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.790A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1675 " --> pdb=" O VAL A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1692 Processing helix chain 'A' and resid 1693 through 1699 Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.583A pdb=" N LEU A1714 " --> pdb=" O LEU A1710 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A1716 " --> pdb=" O ARG A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 removed outlier: 3.619A pdb=" N MET A1743 " --> pdb=" O TYR A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1767 removed outlier: 3.836A pdb=" N LEU A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A1760 " --> pdb=" O PRO A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1787 removed outlier: 3.603A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.692A pdb=" N VAL A1801 " --> pdb=" O LEU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1823 removed outlier: 4.483A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A1821 " --> pdb=" O GLN A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1830 removed outlier: 3.893A pdb=" N HIS A1830 " --> pdb=" O THR A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1853 removed outlier: 3.528A pdb=" N LEU A1836 " --> pdb=" O SER A1832 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1841 " --> pdb=" O ARG A1837 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1882 removed outlier: 3.636A pdb=" N LYS A1869 " --> pdb=" O THR A1865 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A1873 " --> pdb=" O LYS A1869 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A1874 " --> pdb=" O LYS A1870 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1879 " --> pdb=" O LYS A1875 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A1882 " --> pdb=" O ASP A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 4.173A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1902 removed outlier: 4.564A pdb=" N HIS A1901 " --> pdb=" O ASN A1897 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A1902 " --> pdb=" O GLN A1898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1897 through 1902' Processing helix chain 'A' and resid 1909 through 1924 removed outlier: 4.043A pdb=" N ASP A1921 " --> pdb=" O LYS A1917 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1954 removed outlier: 3.590A pdb=" N SER A1950 " --> pdb=" O ASN A1946 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1976 removed outlier: 3.706A pdb=" N LEU A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.625A pdb=" N LYS A2102 " --> pdb=" O THR A2098 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2135 removed outlier: 3.606A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A2131 " --> pdb=" O LYS A2127 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2153 removed outlier: 3.746A pdb=" N LEU A2149 " --> pdb=" O PHE A2145 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A2150 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2154 through 2158 Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 3.714A pdb=" N TRP A2164 " --> pdb=" O TYR A2160 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2185 through 2195 removed outlier: 3.532A pdb=" N ILE A2193 " --> pdb=" O ILE A2189 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2214 Processing helix chain 'A' and resid 2215 through 2222 Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.669A pdb=" N GLU A2258 " --> pdb=" O ARG A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.533A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A2275 " --> pdb=" O SER A2271 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2306 Processing helix chain 'A' and resid 2307 through 2309 No H-bonds generated for 'chain 'A' and resid 2307 through 2309' Processing helix chain 'A' and resid 2312 through 2315 Processing helix chain 'A' and resid 2316 through 2333 removed outlier: 3.593A pdb=" N LEU A2323 " --> pdb=" O ALA A2319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2336 through 2353 removed outlier: 4.118A pdb=" N SER A2340 " --> pdb=" O ILE A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2368 removed outlier: 4.100A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2375 removed outlier: 3.748A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 4.209A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A2396 " --> pdb=" O VAL A2392 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A2401 " --> pdb=" O CYS A2397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A2402 " --> pdb=" O LEU A2398 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2417 removed outlier: 3.985A pdb=" N SER A2417 " --> pdb=" O PHE A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2421 through 2426 removed outlier: 4.233A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS A2426 " --> pdb=" O GLN A2422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2421 through 2426' Processing helix chain 'A' and resid 2428 through 2443 removed outlier: 3.947A pdb=" N VAL A2434 " --> pdb=" O GLU A2430 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A2439 " --> pdb=" O CYS A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.792A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.797A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2507 removed outlier: 4.151A pdb=" N ASP A2504 " --> pdb=" O LYS A2500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A2505 " --> pdb=" O LEU A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2512 Processing helix chain 'A' and resid 2514 through 2526 removed outlier: 3.658A pdb=" N ILE A2520 " --> pdb=" O GLY A2516 " (cutoff:3.500A) Processing helix chain 'A' and resid 2534 through 2542 removed outlier: 3.905A pdb=" N LEU A2539 " --> pdb=" O THR A2535 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A2540 " --> pdb=" O LEU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2556 through 2564 removed outlier: 3.738A pdb=" N ASN A2560 " --> pdb=" O SER A2556 " (cutoff:3.500A) Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix removed outlier: 3.889A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2801 through 2821 Processing helix chain 'A' and resid 2825 through 2846 removed outlier: 3.513A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A2835 " --> pdb=" O ASN A2831 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A2842 " --> pdb=" O GLN A2838 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2864 removed outlier: 3.769A pdb=" N GLN A2859 " --> pdb=" O VAL A2855 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2897 Processing helix chain 'A' and resid 2917 through 2934 removed outlier: 3.719A pdb=" N LEU A2921 " --> pdb=" O PRO A2917 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A2922 " --> pdb=" O PRO A2918 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS A2928 " --> pdb=" O VAL A2924 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 4.300A pdb=" N LEU A2939 " --> pdb=" O GLU A2935 " (cutoff:3.500A) Processing helix chain 'A' and resid 2953 through 2962 removed outlier: 3.687A pdb=" N LEU A2957 " --> pdb=" O THR A2953 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2978 removed outlier: 3.934A pdb=" N GLU A2974 " --> pdb=" O LYS A2970 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 3.767A pdb=" N LEU A2996 " --> pdb=" O ASP A2992 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A3002 " --> pdb=" O SER A2998 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A3005 " --> pdb=" O CYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.995A pdb=" N TYR A3013 " --> pdb=" O LYS A3009 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3045 removed outlier: 3.582A pdb=" N MET A3044 " --> pdb=" O TYR A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3045 through 3054 Processing helix chain 'A' and resid 3059 through 3069 Processing helix chain 'A' and resid 3073 through 3082 removed outlier: 4.199A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.517A pdb=" N LEU A3089 " --> pdb=" O GLU A3085 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A3091 " --> pdb=" O SER A3087 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3114 removed outlier: 3.946A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3130 removed outlier: 3.553A pdb=" N LEU A3126 " --> pdb=" O HIS A3122 " (cutoff:3.500A) Processing helix chain 'A' and resid 3132 through 3147 removed outlier: 3.561A pdb=" N GLU A3137 " --> pdb=" O GLN A3133 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3165 removed outlier: 4.141A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A3163 " --> pdb=" O ARG A3159 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 4.441A pdb=" N ASP A3181 " --> pdb=" O ASN A3177 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A3182 " --> pdb=" O ILE A3178 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A3186 " --> pdb=" O ILE A3182 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A3189 " --> pdb=" O ASN A3185 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A3194 " --> pdb=" O LEU A3190 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A3196 " --> pdb=" O LYS A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3235 removed outlier: 3.791A pdb=" N ILE A3231 " --> pdb=" O ILE A3227 " (cutoff:3.500A) Processing helix chain 'A' and resid 3235 through 3249 removed outlier: 3.813A pdb=" N LYS A3239 " --> pdb=" O LYS A3235 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A3240 " --> pdb=" O PHE A3236 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A3241 " --> pdb=" O SER A3237 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3263 removed outlier: 4.241A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A3262 " --> pdb=" O LEU A3258 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A3263 " --> pdb=" O LEU A3259 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3287 removed outlier: 3.520A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A3275 " --> pdb=" O ASP A3271 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3298 Processing helix chain 'A' and resid 3298 through 3307 removed outlier: 4.297A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 3.559A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A3338 " --> pdb=" O TYR A3334 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3352 removed outlier: 3.968A pdb=" N GLU A3350 " --> pdb=" O ALA A3346 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A3351 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3364 removed outlier: 3.540A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A3361 " --> pdb=" O ARG A3357 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3392 removed outlier: 3.832A pdb=" N GLN A3383 " --> pdb=" O GLN A3379 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS A3384 " --> pdb=" O ARG A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3407 through 3428 removed outlier: 3.512A pdb=" N GLN A3423 " --> pdb=" O PHE A3419 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.510A pdb=" N LEU A3451 " --> pdb=" O VAL A3447 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A3452 " --> pdb=" O GLU A3448 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3463 Processing helix chain 'A' and resid 3464 through 3472 removed outlier: 4.053A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 4.029A pdb=" N THR A3484 " --> pdb=" O LEU A3480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3504 through 3506 No H-bonds generated for 'chain 'A' and resid 3504 through 3506' Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.570A pdb=" N GLU A3519 " --> pdb=" O GLN A3515 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A3520 " --> pdb=" O HIS A3516 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 Processing helix chain 'A' and resid 3547 through 3563 removed outlier: 4.264A pdb=" N ARG A3557 " --> pdb=" O GLU A3553 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 removed outlier: 4.104A pdb=" N LEU A3575 " --> pdb=" O PHE A3571 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3595 removed outlier: 3.680A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3617 removed outlier: 3.617A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A3614 " --> pdb=" O TYR A3610 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.784A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3658 through 3673 removed outlier: 3.771A pdb=" N LYS A3669 " --> pdb=" O MET A3665 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A3670 " --> pdb=" O LEU A3666 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A3671 " --> pdb=" O LEU A3667 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) Processing helix chain 'A' and resid 3680 through 3684 Processing helix chain 'A' and resid 3758 through 3764 Processing helix chain 'A' and resid 3766 through 3769 Processing helix chain 'A' and resid 3770 through 3775 Processing helix chain 'A' and resid 3778 through 3783 Processing helix chain 'A' and resid 3812 through 3818 Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 4.025A pdb=" N TYR A3828 " --> pdb=" O GLU A3824 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3847 removed outlier: 3.991A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.583A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3878 removed outlier: 3.883A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 removed outlier: 3.581A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 4.047A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A3905 " --> pdb=" O ARG A3901 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A3906 " --> pdb=" O SER A3902 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A3909 " --> pdb=" O ALA A3905 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3969 removed outlier: 3.509A pdb=" N ILE A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.953A pdb=" N HIS A3986 " --> pdb=" O SER A3982 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4007 removed outlier: 3.841A pdb=" N ASN A4000 " --> pdb=" O GLY A3996 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A4001 " --> pdb=" O LEU A3997 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A4005 " --> pdb=" O THR A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.708A pdb=" N GLN A4018 " --> pdb=" O LYS A4014 " (cutoff:3.500A) Processing helix chain 'A' and resid 4040 through 4053 removed outlier: 4.667A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A4051 " --> pdb=" O ALA A4047 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A4053 " --> pdb=" O ARG A4049 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 removed outlier: 3.600A pdb=" N THR A4060 " --> pdb=" O PRO A4056 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A4066 " --> pdb=" O ASP A4062 " (cutoff:3.500A) Processing helix chain 'A' and resid 4073 through 4082 removed outlier: 3.694A pdb=" N ALA A4079 " --> pdb=" O ARG A4075 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4108 removed outlier: 3.639A pdb=" N VAL A4104 " --> pdb=" O GLU A4100 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A4105 " --> pdb=" O GLU A4101 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 5010 through 5014 removed outlier: 4.026A pdb=" N UNK A5013 " --> pdb=" O UNK A5010 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N UNK A5014 " --> pdb=" O UNK A5011 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5010 through 5014' Processing helix chain 'A' and resid 6007 through 6012 removed outlier: 3.951A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNK A6012 " --> pdb=" O UNK A6008 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6007 through 6012' Processing helix chain 'A' and resid 6014 through 6019 Processing helix chain 'B' and resid 721 through 732 Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 3.516A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A3803 " --> pdb=" O LEU A3751 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3809 through 3811 1357 hydrogen bonds defined for protein. 3999 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: 16.05 Time building geometry restraints manager: 12.71 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: 9460 1.34 - 1.46: 6487 1.46 - 1.58: 13548 1.58 - 1.70: 0 1.70 - 1.82: 299 Bond restraints: 29794 Sorted by residual: bond pdb=" C ARG A 257 " pdb=" N PRO A 258 " ideal model delta sigma weight residual 1.332 1.356 -0.024 8.20e-03 1.49e+04 8.26e+00 bond pdb=" C ALA A 101 " pdb=" N PRO A 102 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.95e+00 bond pdb=" C LEU A3041 " pdb=" N PRO A3042 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.74e+00 bond pdb=" CB PRO A3685 " pdb=" CG PRO A3685 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.55e+00 bond pdb=" SD MET A2473 " pdb=" CE MET A2473 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.58e+00 ... (remaining 29789 not shown) Histogram of bond angle deviations from ideal: 92.77 - 101.05: 66 101.05 - 109.32: 1970 109.32 - 117.59: 19936 117.59 - 125.86: 17915 125.86 - 134.14: 417 Bond angle restraints: 40304 Sorted by residual: angle pdb=" N VAL A1659 " pdb=" CA VAL A1659 " pdb=" C VAL A1659 " ideal model delta sigma weight residual 113.71 107.70 6.01 9.50e-01 1.11e+00 4.00e+01 angle pdb=" CG MET A1880 " pdb=" SD MET A1880 " pdb=" CE MET A1880 " ideal model delta sigma weight residual 100.90 92.77 8.13 2.20e+00 2.07e-01 1.36e+01 angle pdb=" C ILE A 100 " pdb=" N ALA A 101 " pdb=" CA ALA A 101 " ideal model delta sigma weight residual 121.80 112.91 8.89 2.44e+00 1.68e-01 1.33e+01 angle pdb=" C ASP A2492 " pdb=" N ASN A2493 " pdb=" CA ASN A2493 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 ... (remaining 40299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 16238 17.82 - 35.64: 1595 35.64 - 53.46: 259 53.46 - 71.28: 56 71.28 - 89.10: 22 Dihedral angle restraints: 18170 sinusoidal: 7273 harmonic: 10897 Sorted by residual: dihedral pdb=" CA LYS A 722 " pdb=" C LYS A 722 " pdb=" N ASP A 723 " pdb=" CA ASP A 723 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ALA A 101 " pdb=" C ALA A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER A3539 " pdb=" C SER A3539 " pdb=" N TYR A3540 " pdb=" CA TYR A3540 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 18167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3191 0.040 - 0.079: 1156 0.079 - 0.119: 223 0.119 - 0.158: 27 0.158 - 0.198: 2 Chirality restraints: 4599 Sorted by residual: chirality pdb=" CA VAL A2310 " pdb=" N VAL A2310 " pdb=" C VAL A2310 " pdb=" CB VAL A2310 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA ASN A2493 " pdb=" N ASN A2493 " pdb=" C ASN A2493 " pdb=" CB ASN A2493 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA ILE A2294 " pdb=" N ILE A2294 " pdb=" C ILE A2294 " pdb=" CB ILE A2294 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 4596 not shown) Planarity restraints: 5128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1970 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO A1971 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A1971 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A1971 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1378 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A1379 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A1379 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1379 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1178 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A1179 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A1179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1179 " 0.039 5.00e-02 4.00e+02 ... (remaining 5125 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1159 2.72 - 3.26: 33406 3.26 - 3.81: 46488 3.81 - 4.35: 58605 4.35 - 4.90: 92876 Nonbonded interactions: 232534 Sorted by model distance: nonbonded pdb=" OE1 GLU A2578 " pdb=" ND1 HIS A2579 " model vdw 2.170 2.520 nonbonded pdb=" OH TYR A1675 " pdb=" O ALA A1692 " model vdw 2.205 2.440 nonbonded pdb=" NH1 ARG A1151 " pdb=" O LEU A1163 " model vdw 2.209 2.520 nonbonded pdb=" O GLY A2879 " pdb=" OG SER A2883 " model vdw 2.210 2.440 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.215 2.520 ... (remaining 232529 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=0.00 max=1.00 mean=0.96 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.020 Extract box with map and model: 9.550 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 79.300 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.080 29794 Z= 0.231 Angle : 0.680 9.388 40304 Z= 0.366 Chirality : 0.040 0.198 4599 Planarity : 0.005 0.105 5128 Dihedral : 14.435 89.102 11064 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.74 (0.13), residues: 3641 helix: -1.46 (0.11), residues: 2100 sheet: -2.56 (0.67), residues: 50 loop : -2.18 (0.16), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3884 time to fit residues: 82.0411 Evaluate side-chains 116 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2270 ASN A2365 ASN A2799 GLN A2841 ASN A3093 GLN ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4000 ASN A4042 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 29794 Z= 0.354 Angle : 0.736 8.933 40304 Z= 0.382 Chirality : 0.042 0.185 4599 Planarity : 0.005 0.061 5128 Dihedral : 5.213 29.243 3964 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.98 % Favored : 90.94 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3641 helix: -0.56 (0.11), residues: 2265 sheet: -2.12 (0.65), residues: 50 loop : -2.34 (0.17), residues: 1326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 120 average time/residue: 0.4304 time to fit residues: 89.6867 Evaluate side-chains 116 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2485 time to fit residues: 5.6655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 8.9990 chunk 104 optimal weight: 0.1980 chunk 279 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 chunk 363 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 270 optimal weight: 0.1980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3787 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29794 Z= 0.170 Angle : 0.596 8.738 40304 Z= 0.304 Chirality : 0.039 0.181 4599 Planarity : 0.004 0.049 5128 Dihedral : 4.819 26.570 3964 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.91 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3641 helix: 0.03 (0.11), residues: 2252 sheet: -2.21 (0.61), residues: 52 loop : -2.10 (0.18), residues: 1337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 131 average time/residue: 0.4211 time to fit residues: 98.4535 Evaluate side-chains 117 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2655 time to fit residues: 5.9403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 0.0570 chunk 226 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 357 optimal weight: 0.3980 chunk 176 optimal weight: 0.3980 chunk 320 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1331 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 GLN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 29794 Z= 0.163 Angle : 0.585 8.719 40304 Z= 0.294 Chirality : 0.038 0.185 4599 Planarity : 0.004 0.048 5128 Dihedral : 4.643 26.580 3964 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.64 % Favored : 92.28 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.91 (0.14), residues: 3641 helix: 0.29 (0.11), residues: 2267 sheet: -2.00 (0.63), residues: 52 loop : -2.09 (0.18), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 142 average time/residue: 0.3943 time to fit residues: 97.1437 Evaluate side-chains 121 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 3.586 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2898 time to fit residues: 8.7217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 147 optimal weight: 0.4980 chunk 305 optimal weight: 0.4980 chunk 247 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 182 optimal weight: 1.9990 chunk 321 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2508 GLN ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 29794 Z= 0.143 Angle : 0.583 8.737 40304 Z= 0.290 Chirality : 0.038 0.264 4599 Planarity : 0.004 0.051 5128 Dihedral : 4.469 26.839 3964 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.13 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.69 (0.14), residues: 3641 helix: 0.48 (0.11), residues: 2277 sheet: -1.79 (0.64), residues: 52 loop : -2.06 (0.18), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 139 average time/residue: 0.4036 time to fit residues: 97.9489 Evaluate side-chains 126 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2974 time to fit residues: 10.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 8.9990 chunk 322 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 357 optimal weight: 0.0980 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29794 Z= 0.165 Angle : 0.579 8.498 40304 Z= 0.287 Chirality : 0.038 0.204 4599 Planarity : 0.004 0.051 5128 Dihedral : 4.375 26.160 3964 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.61 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.49 (0.15), residues: 3641 helix: 0.66 (0.11), residues: 2285 sheet: -1.67 (0.64), residues: 52 loop : -2.05 (0.18), residues: 1304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 131 average time/residue: 0.3970 time to fit residues: 91.0701 Evaluate side-chains 119 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2729 time to fit residues: 6.4864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 6.9990 chunk 40 optimal weight: 0.0670 chunk 203 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 356 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1331 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29794 Z= 0.196 Angle : 0.606 12.035 40304 Z= 0.299 Chirality : 0.038 0.188 4599 Planarity : 0.004 0.052 5128 Dihedral : 4.364 25.678 3964 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.31 % Favored : 92.64 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.29 (0.15), residues: 3641 helix: 0.80 (0.11), residues: 2289 sheet: -1.58 (0.74), residues: 40 loop : -1.95 (0.18), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.4466 time to fit residues: 99.0383 Evaluate side-chains 123 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2752 time to fit residues: 9.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 242 optimal weight: 0.0970 chunk 176 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 ASN A1331 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4088 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 29794 Z= 0.163 Angle : 0.600 12.380 40304 Z= 0.293 Chirality : 0.038 0.188 4599 Planarity : 0.004 0.053 5128 Dihedral : 4.324 25.588 3964 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.24 (0.15), residues: 3641 helix: 0.86 (0.11), residues: 2302 sheet: -1.44 (0.67), residues: 52 loop : -1.99 (0.18), residues: 1287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 127 average time/residue: 0.4351 time to fit residues: 96.3887 Evaluate side-chains 121 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 3.930 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3414 time to fit residues: 8.9923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 9.9990 chunk 341 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 332 optimal weight: 0.0050 chunk 200 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 ASN A1115 HIS ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 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: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29794 Z= 0.168 Angle : 0.624 13.872 40304 Z= 0.303 Chirality : 0.039 0.252 4599 Planarity : 0.004 0.053 5128 Dihedral : 4.300 25.366 3964 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.20 % Favored : 92.75 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3641 helix: 0.93 (0.11), residues: 2300 sheet: -1.39 (0.75), residues: 40 loop : -1.98 (0.18), residues: 1301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.4333 time to fit residues: 89.5953 Evaluate side-chains 115 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 10.0000 chunk 351 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 339 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 ASN A1331 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29794 Z= 0.191 Angle : 0.637 12.908 40304 Z= 0.309 Chirality : 0.039 0.224 4599 Planarity : 0.004 0.052 5128 Dihedral : 4.333 25.463 3964 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3641 helix: 0.97 (0.11), residues: 2306 sheet: -1.33 (0.76), residues: 40 loop : -2.00 (0.18), residues: 1295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7282 Ramachandran restraints generated. 3641 Oldfield, 0 Emsley, 3641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 119 average time/residue: 0.4281 time to fit residues: 89.0195 Evaluate side-chains 116 residues out of total 3289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 6.9990 chunk 312 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 293 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 301 optimal weight: 0.5980 chunk 37 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 ASN A1331 ASN ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.047337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038743 restraints weight = 289052.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039799 restraints weight = 155366.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.040571 restraints weight = 103020.561| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 29794 Z= 0.162 Angle : 0.628 13.357 40304 Z= 0.302 Chirality : 0.039 0.217 4599 Planarity : 0.004 0.053 5128 Dihedral : 4.274 24.910 3964 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.05 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.08 (0.15), residues: 3641 helix: 1.00 (0.11), residues: 2311 sheet: -1.21 (0.77), residues: 40 loop : -2.01 (0.18), residues: 1290 =============================================================================== Job complete usr+sys time: 3810.28 seconds wall clock time: 72 minutes 11.49 seconds (4331.49 seconds total)