Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 12:52:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otv_13067/08_2023/7otv_13067_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 191 5.16 5 C 18632 2.51 5 N 4903 2.21 5 O 5315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 891": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1775": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A ARG 1937": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A ARG 2090": "NH1" <-> "NH2" Residue "A ARG 2106": "NH1" <-> "NH2" Residue "A ARG 2120": "NH1" <-> "NH2" Residue "A GLU 2154": "OE1" <-> "OE2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A GLU 2236": "OE1" <-> "OE2" Residue "A GLU 2243": "OE1" <-> "OE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A GLU 2321": "OE1" <-> "OE2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2406": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2819": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 2925": "OE1" <-> "OE2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 3038": "OE1" <-> "OE2" Residue "A GLU 3137": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A GLU 3295": "OE1" <-> "OE2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3350": "OE1" <-> "OE2" Residue "A GLU 3353": "OE1" <-> "OE2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A GLU 3393": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3428": "OE1" <-> "OE2" Residue "A GLU 3460": "OE1" <-> "OE2" Residue "A GLU 3478": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3724": "OE1" <-> "OE2" Residue "A ARG 3725": "NH1" <-> "NH2" Residue "A ARG 3741": "NH1" <-> "NH2" Residue "A GLU 3745": "OE1" <-> "OE2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A GLU 3875": "OE1" <-> "OE2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A GLU 4093": "OE1" <-> "OE2" Residue "A ARG 4119": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 29041 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3657, 29041 Unusual residues: {'KWT': 1} Classifications: {'peptide': 3656, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 158, 'TRANS': 3497, None: 1} Not linked: pdbres="UNK A6020 " pdbres="KWT A6101 " Chain breaks: 17 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'UNK:plan-1': 20, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 14.36, per 1000 atoms: 0.49 Number of scatterers: 29041 At special positions: 0 Unit cell: (122.576, 156.48, 183.864, 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 191 16.00 O 5315 8.00 N 4903 7.00 C 18632 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.42 Conformation dependent library (CDL) restraints added in 4.4 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 4 sheets defined 61.9% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 4.988A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.745A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.761A pdb=" N THR A 55 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 72 removed outlier: 3.562A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.544A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.812A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.384A pdb=" N LEU A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.543A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.591A pdb=" N LEU A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.940A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.811A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 291 through 301 removed outlier: 4.069A pdb=" N VAL A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 357 through 368 removed outlier: 3.855A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.692A pdb=" N CYS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 423 removed outlier: 4.235A pdb=" N TYR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Proline residue: A 433 - end of helix removed outlier: 4.138A pdb=" N VAL A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A 440 " --> pdb=" O HIS A 437 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 444 " --> pdb=" O MET A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 4.242A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 removed outlier: 4.303A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.642A pdb=" N ALA A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 removed outlier: 3.601A pdb=" N LYS A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 removed outlier: 4.002A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 643 through 659 removed outlier: 3.590A pdb=" N VAL A 646 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 650 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 651 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 652 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 654 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU A 655 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 658 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 removed outlier: 3.514A pdb=" N TYR A 667 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 669 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 671 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE A 672 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG A 675 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 676 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 679 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 719 removed outlier: 3.518A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.653A pdb=" N THR A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.925A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 Proline residue: A 750 - end of helix removed outlier: 3.934A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.587A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 804 Proline residue: A 787 - end of helix removed outlier: 4.837A pdb=" N LYS A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP A 791 " --> pdb=" O PRO A 787 " (cutoff:3.500A) Proline residue: A 794 - end of helix removed outlier: 3.879A pdb=" N ASP A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR A 799 " --> pdb=" O CYS A 795 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 803 " --> pdb=" O TYR A 799 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.591A pdb=" N VAL A 873 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A 874 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 920 Proline residue: A 912 - end of helix removed outlier: 4.813A pdb=" N THR A 915 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 918 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 919 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 944 Processing helix chain 'A' and resid 959 through 973 removed outlier: 3.823A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 978 through 995 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1008 through 1011 No H-bonds generated for 'chain 'A' and resid 1008 through 1011' Processing helix chain 'A' and resid 1024 through 1043 removed outlier: 3.635A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1031 " --> pdb=" O ASP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1050 removed outlier: 4.155A pdb=" N GLU A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1076 through 1085 removed outlier: 3.690A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1116 removed outlier: 3.645A pdb=" N GLN A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1140 Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'A' and resid 1165 through 1174 Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1214 Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.845A pdb=" N ILE A1221 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU A1225 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1271 removed outlier: 3.573A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1290 through 1299 removed outlier: 3.942A pdb=" N GLU A1299 " --> pdb=" O ALA A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1350 removed outlier: 3.704A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.991A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1360' Processing helix chain 'A' and resid 1365 through 1377 removed outlier: 4.180A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1382 Processing helix chain 'A' and resid 1391 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.770A pdb=" N ASN A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1442 through 1461 Processing helix chain 'A' and resid 1464 through 1467 No H-bonds generated for 'chain 'A' and resid 1464 through 1467' Processing helix chain 'A' and resid 1477 through 1480 No H-bonds generated for 'chain 'A' and resid 1477 through 1480' Processing helix chain 'A' and resid 1482 through 1485 No H-bonds generated for 'chain 'A' and resid 1482 through 1485' Processing helix chain 'A' and resid 1507 through 1519 Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.620A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1562 Processing helix chain 'A' and resid 1564 through 1573 removed outlier: 3.716A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A1570 " --> pdb=" O THR A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1585 removed outlier: 4.402A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1605 Processing helix chain 'A' and resid 1612 through 1624 removed outlier: 3.554A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1629 Processing helix chain 'A' and resid 1639 through 1655 Processing helix chain 'A' and resid 1668 through 1679 Processing helix chain 'A' and resid 1686 through 1699 removed outlier: 4.312A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A1696 " --> pdb=" O ALA A1692 " (cutoff:3.500A) Proline residue: A1697 - end of helix Processing helix chain 'A' and resid 1707 through 1721 Processing helix chain 'A' and resid 1734 through 1753 Processing helix chain 'A' and resid 1756 through 1768 removed outlier: 3.656A pdb=" N ARG A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1785 Processing helix chain 'A' and resid 1791 through 1805 Processing helix chain 'A' and resid 1813 through 1821 removed outlier: 3.719A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 4.609A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1881 removed outlier: 3.769A pdb=" N TYR A1881 " --> pdb=" O ASP A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1889 No H-bonds generated for 'chain 'A' and resid 1886 through 1889' Processing helix chain 'A' and resid 1911 through 1923 removed outlier: 3.853A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE A1923 " --> pdb=" O CYS A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1955 removed outlier: 3.578A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1971 through 1974 No H-bonds generated for 'chain 'A' and resid 1971 through 1974' Processing helix chain 'A' and resid 2094 through 2105 Processing helix chain 'A' and resid 2124 through 2134 removed outlier: 3.625A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2171 removed outlier: 3.551A pdb=" N ARG A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) Proline residue: A2159 - end of helix removed outlier: 5.195A pdb=" N LYS A2162 " --> pdb=" O ARG A2158 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A2163 " --> pdb=" O PRO A2159 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2184 through 2195 Processing helix chain 'A' and resid 2206 through 2221 removed outlier: 4.009A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2255 through 2260 removed outlier: 3.515A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2255 through 2260' Processing helix chain 'A' and resid 2268 through 2282 removed outlier: 3.791A pdb=" N VAL A2272 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 4.032A pdb=" N ASN A2306 " --> pdb=" O ALA A2302 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N MET A2307 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 removed outlier: 3.799A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 4.188A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2369 removed outlier: 4.028A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2388 removed outlier: 3.747A pdb=" N ASP A2376 " --> pdb=" O PRO A2373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A2379 " --> pdb=" O ASP A2376 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN A2380 " --> pdb=" O ARG A2377 " (cutoff:3.500A) Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2403 Processing helix chain 'A' and resid 2414 through 2417 No H-bonds generated for 'chain 'A' and resid 2414 through 2417' Processing helix chain 'A' and resid 2420 through 2425 removed outlier: 3.521A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A2425 " --> pdb=" O VAL A2421 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2420 through 2425' Processing helix chain 'A' and resid 2430 through 2445 removed outlier: 3.597A pdb=" N CYS A2435 " --> pdb=" O ARG A2431 " (cutoff:3.500A) Proline residue: A2444 - end of helix Processing helix chain 'A' and resid 2448 through 2461 removed outlier: 3.925A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 4.047A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2470 through 2483 removed outlier: 3.731A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2511 removed outlier: 3.775A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A2510 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A2511 " --> pdb=" O ILE A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2525 Processing helix chain 'A' and resid 2535 through 2545 removed outlier: 4.054A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2558 through 2565 removed outlier: 4.251A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2787 through 2798 removed outlier: 3.831A pdb=" N ILE A2791 " --> pdb=" O SER A2788 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR A2792 " --> pdb=" O SER A2789 " (cutoff:3.500A) Proline residue: A2793 - end of helix removed outlier: 3.653A pdb=" N VAL A2797 " --> pdb=" O LEU A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2802 through 2819 Processing helix chain 'A' and resid 2826 through 2845 Processing helix chain 'A' and resid 2852 through 2863 Processing helix chain 'A' and resid 2868 through 2870 No H-bonds generated for 'chain 'A' and resid 2868 through 2870' Processing helix chain 'A' and resid 2873 through 2882 Processing helix chain 'A' and resid 2886 through 2899 removed outlier: 3.515A pdb=" N LEU A2898 " --> pdb=" O GLU A2894 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2933 removed outlier: 3.579A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2943 removed outlier: 3.524A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) Processing helix chain 'A' and resid 2954 through 2961 removed outlier: 3.546A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 4.424A pdb=" N LEU A2999 " --> pdb=" O GLU A2995 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A3000 " --> pdb=" O LEU A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3013 Processing helix chain 'A' and resid 3041 through 3053 removed outlier: 3.504A pdb=" N SER A3047 " --> pdb=" O TYR A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3070 Processing helix chain 'A' and resid 3075 through 3080 Processing helix chain 'A' and resid 3083 through 3093 removed outlier: 3.705A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3096 through 3115 Processing helix chain 'A' and resid 3122 through 3145 removed outlier: 3.568A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A3128 " --> pdb=" O SER A3124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A3140 " --> pdb=" O THR A3136 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 removed outlier: 3.609A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) Processing helix chain 'A' and resid 3176 through 3195 removed outlier: 3.957A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 3.979A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3254 through 3261 Processing helix chain 'A' and resid 3272 through 3286 removed outlier: 3.765A pdb=" N ARG A3282 " --> pdb=" O GLN A3278 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A3283 " --> pdb=" O SER A3279 " (cutoff:3.500A) Processing helix chain 'A' and resid 3291 through 3306 removed outlier: 4.577A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN A3296 " --> pdb=" O GLY A3292 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) Processing helix chain 'A' and resid 3323 through 3343 Processing helix chain 'A' and resid 3346 through 3351 removed outlier: 4.092A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3355 through 3363 removed outlier: 3.982A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3370 through 3393 Processing helix chain 'A' and resid 3406 through 3429 Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 3.502A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) Processing helix chain 'A' and resid 3459 through 3463 Processing helix chain 'A' and resid 3465 through 3471 removed outlier: 3.824A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A3470 " --> pdb=" O PRO A3466 " (cutoff:3.500A) Processing helix chain 'A' and resid 3476 through 3479 Processing helix chain 'A' and resid 3483 through 3489 removed outlier: 3.544A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER A3489 " --> pdb=" O LYS A3485 " (cutoff:3.500A) Processing helix chain 'A' and resid 3499 through 3505 removed outlier: 4.132A pdb=" N ALA A3504 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A3505 " --> pdb=" O HIS A3501 " (cutoff:3.500A) Processing helix chain 'A' and resid 3515 through 3524 removed outlier: 3.537A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3537 Processing helix chain 'A' and resid 3548 through 3562 removed outlier: 4.249A pdb=" N LYS A3552 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A3553 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3567 through 3576 Processing helix chain 'A' and resid 3581 through 3593 Processing helix chain 'A' and resid 3606 through 3616 removed outlier: 3.725A pdb=" N ALA A3615 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3627 through 3635 removed outlier: 3.688A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3643 No H-bonds generated for 'chain 'A' and resid 3640 through 3643' Processing helix chain 'A' and resid 3650 through 3652 No H-bonds generated for 'chain 'A' and resid 3650 through 3652' Processing helix chain 'A' and resid 3658 through 3673 removed outlier: 3.565A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A3672 " --> pdb=" O LEU A3668 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A3673 " --> pdb=" O LYS A3669 " (cutoff:3.500A) Processing helix chain 'A' and resid 3681 through 3684 No H-bonds generated for 'chain 'A' and resid 3681 through 3684' Processing helix chain 'A' and resid 3687 through 3689 No H-bonds generated for 'chain 'A' and resid 3687 through 3689' Processing helix chain 'A' and resid 3759 through 3776 Processing helix chain 'A' and resid 3780 through 3783 No H-bonds generated for 'chain 'A' and resid 3780 through 3783' Processing helix chain 'A' and resid 3812 through 3819 removed outlier: 3.585A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3846 removed outlier: 4.063A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3854 through 3861 removed outlier: 3.919A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3866 through 3877 removed outlier: 3.654A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3894 through 3917 removed outlier: 3.995A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3948 through 3951 No H-bonds generated for 'chain 'A' and resid 3948 through 3951' Processing helix chain 'A' and resid 3965 through 3968 No H-bonds generated for 'chain 'A' and resid 3965 through 3968' Processing helix chain 'A' and resid 3979 through 3993 removed outlier: 3.608A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A3986 " --> pdb=" O SER A3982 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4006 Processing helix chain 'A' and resid 4013 through 4021 Processing helix chain 'A' and resid 4044 through 4049 Processing helix chain 'A' and resid 4056 through 4067 removed outlier: 3.593A pdb=" N CYS A4061 " --> pdb=" O ALA A4057 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4102 through 4111 removed outlier: 3.663A pdb=" N LEU A4107 " --> pdb=" O GLN A4103 " (cutoff:3.500A) Processing helix chain 'A' and resid 4114 through 4119 removed outlier: 4.417A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'A' and resid 6003 through 6009 removed outlier: 3.646A pdb=" N UNK A6007 " --> pdb=" O UNK A6003 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK A6008 " --> pdb=" O UNK A6004 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N UNK A6009 " --> pdb=" O UNK A6005 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6003 through 6009' Processing sheet with id= A, first strand: chain 'A' and resid 583 through 585 Processing sheet with id= B, first strand: chain 'A' and resid 893 through 895 Processing sheet with id= C, first strand: chain 'A' and resid 3737 through 3742 removed outlier: 4.163A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A3797 " --> pdb=" O LEU A3800 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 3809 through 3811 1258 hydrogen bonds defined for protein. 3405 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: 12.79 Time building geometry restraints manager: 13.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.57: 29329 1.57 - 1.95: 306 1.95 - 2.33: 0 2.33 - 2.71: 0 2.71 - 3.09: 1 Bond restraints: 29636 Sorted by residual: bond pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " ideal model delta sigma weight residual 1.399 3.092 -1.693 2.00e-02 2.50e+03 7.17e+03 bond pdb=" C11 KWT A6101 " pdb=" C8 KWT A6101 " ideal model delta sigma weight residual 1.392 1.611 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C16 KWT A6101 " pdb=" C17 KWT A6101 " ideal model delta sigma weight residual 1.677 1.522 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C17 KWT A6101 " pdb=" C18 KWT A6101 " ideal model delta sigma weight residual 1.410 1.537 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C13 KWT A6101 " pdb=" C18 KWT A6101 " ideal model delta sigma weight residual 1.629 1.511 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 29631 not shown) Histogram of bond angle deviations from ideal: 72.73 - 85.03: 2 85.03 - 97.33: 0 97.33 - 109.64: 3019 109.64 - 121.94: 31772 121.94 - 134.24: 5294 Bond angle restraints: 40087 Sorted by residual: angle pdb=" C3 KWT A6101 " pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " ideal model delta sigma weight residual 108.08 72.73 35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C19 KWT A6101 " pdb=" O5 KWT A6101 " pdb=" C5 KWT A6101 " ideal model delta sigma weight residual 108.06 81.37 26.69 3.00e+00 1.11e-01 7.91e+01 angle pdb=" N MET A3483 " pdb=" CA MET A3483 " pdb=" C MET A3483 " ideal model delta sigma weight residual 111.11 121.23 -10.12 1.20e+00 6.94e-01 7.11e+01 angle pdb=" C19 KWT A6101 " pdb=" C3 KWT A6101 " pdb=" C4 KWT A6101 " ideal model delta sigma weight residual 108.05 132.11 -24.06 3.00e+00 1.11e-01 6.43e+01 angle pdb=" C16 KWT A6101 " pdb=" C15 KWT A6101 " pdb=" C7 KWT A6101 " ideal model delta sigma weight residual 102.55 122.89 -20.34 3.00e+00 1.11e-01 4.60e+01 ... (remaining 40082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 16136 17.62 - 35.24: 1588 35.24 - 52.87: 278 52.87 - 70.49: 53 70.49 - 88.11: 21 Dihedral angle restraints: 18076 sinusoidal: 7319 harmonic: 10757 Sorted by residual: dihedral pdb=" CA ILE A2785 " pdb=" C ILE A2785 " pdb=" N LYS A2786 " pdb=" CA LYS A2786 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA LEU A3480 " pdb=" C LEU A3480 " pdb=" N SER A3481 " pdb=" CA SER A3481 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA TYR A3315 " pdb=" C TYR A3315 " pdb=" N LEU A3316 " pdb=" CA LEU A3316 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 18073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.117: 4568 1.117 - 2.233: 0 2.233 - 3.350: 0 3.350 - 4.467: 0 4.467 - 5.584: 1 Chirality restraints: 4569 Sorted by residual: chirality pdb=" C15 KWT A6101 " pdb=" C13 KWT A6101 " pdb=" C16 KWT A6101 " pdb=" C7 KWT A6101 " both_signs ideal model delta sigma weight residual False 2.99 -2.60 5.58 2.00e-01 2.50e+01 7.79e+02 chirality pdb=" C13 KWT A6101 " pdb=" C12 KWT A6101 " pdb=" C15 KWT A6101 " pdb=" C18 KWT A6101 " both_signs ideal model delta sigma weight residual False -2.47 -3.16 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA MET A3483 " pdb=" N MET A3483 " pdb=" C MET A3483 " pdb=" CB MET A3483 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.95e+00 ... (remaining 4566 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 KWT A6101 " 0.418 2.00e-02 2.50e+03 2.69e-01 1.45e+03 pdb=" C2 KWT A6101 " -0.512 2.00e-02 2.50e+03 pdb=" C3 KWT A6101 " 0.070 2.00e-02 2.50e+03 pdb=" C4 KWT A6101 " 0.091 2.00e-02 2.50e+03 pdb=" C5 KWT A6101 " -0.056 2.00e-02 2.50e+03 pdb=" C6 KWT A6101 " -0.045 2.00e-02 2.50e+03 pdb=" C9 KWT A6101 " 0.264 2.00e-02 2.50e+03 pdb=" O5 KWT A6101 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A3727 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C THR A3727 " 0.075 2.00e-02 2.50e+03 pdb=" O THR A3727 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A3728 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1409 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A1410 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1410 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1410 " 0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 431 2.65 - 3.21: 29396 3.21 - 3.78: 44400 3.78 - 4.34: 60614 4.34 - 4.90: 98109 Nonbonded interactions: 232950 Sorted by model distance: nonbonded pdb=" OG1 THR A3809 " pdb=" CE MET A3929 " model vdw 2.090 3.460 nonbonded pdb=" CB THR A3809 " pdb=" CE MET A3929 " model vdw 2.161 3.890 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.198 2.520 nonbonded pdb=" O GLU A 203 " pdb=" OG1 THR A 206 " model vdw 2.198 2.440 nonbonded pdb=" O ALA A2796 " pdb=" NH1 ARG A2800 " model vdw 2.209 2.520 ... (remaining 232945 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=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 6.590 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 76.550 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.693 29636 Z= 0.758 Angle : 0.787 35.352 40087 Z= 0.400 Chirality : 0.095 5.584 4569 Planarity : 0.005 0.269 5088 Dihedral : 14.435 88.111 11064 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.47 % Favored : 91.42 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3602 helix: -0.04 (0.11), residues: 2316 sheet: -1.08 (0.70), residues: 47 loop : -2.13 (0.18), residues: 1239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 742 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 748 average time/residue: 0.4719 time to fit residues: 541.0771 Evaluate side-chains 383 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 3.381 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4357 time to fit residues: 6.0082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 331 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS A 753 GLN A 857 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1175 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN A2456 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2807 GLN A3004 HIS ** A3104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3390 GLN A3527 GLN A3580 ASN A3766 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 29636 Z= 0.242 Angle : 0.705 14.484 40087 Z= 0.347 Chirality : 0.043 0.317 4569 Planarity : 0.005 0.046 5088 Dihedral : 5.067 36.319 3926 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.09 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3602 helix: 0.09 (0.11), residues: 2291 sheet: -0.87 (0.71), residues: 52 loop : -2.04 (0.17), residues: 1259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 404 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 28 residues processed: 451 average time/residue: 0.4384 time to fit residues: 315.6993 Evaluate side-chains 348 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 320 time to evaluate : 3.783 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.2890 time to fit residues: 19.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 358 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 ASN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2865 HIS A3390 GLN A3470 GLN A3766 GLN ** A3951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29636 Z= 0.212 Angle : 0.661 16.671 40087 Z= 0.323 Chirality : 0.041 0.204 4569 Planarity : 0.004 0.045 5088 Dihedral : 4.821 44.330 3926 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.64 % Favored : 93.25 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3602 helix: 0.17 (0.11), residues: 2287 sheet: -0.75 (0.70), residues: 52 loop : -1.99 (0.17), residues: 1263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 348 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 379 average time/residue: 0.4214 time to fit residues: 257.5348 Evaluate side-chains 311 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 3.400 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.3251 time to fit residues: 17.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 315 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2954 GLN A3059 GLN A4110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 29636 Z= 0.308 Angle : 0.700 16.452 40087 Z= 0.344 Chirality : 0.043 0.224 4569 Planarity : 0.005 0.055 5088 Dihedral : 4.910 45.570 3926 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.06 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.04 (0.14), residues: 3602 helix: 0.07 (0.11), residues: 2306 sheet: -0.60 (0.72), residues: 52 loop : -2.09 (0.17), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 325 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 370 average time/residue: 0.4225 time to fit residues: 255.5914 Evaluate side-chains 314 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 3.478 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.3072 time to fit residues: 24.3763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 301 optimal weight: 3.9990 chunk 243 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 316 optimal weight: 9.9990 chunk 89 optimal weight: 0.0770 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 394 GLN A 533 HIS ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29636 Z= 0.192 Angle : 0.632 16.634 40087 Z= 0.308 Chirality : 0.040 0.180 4569 Planarity : 0.004 0.042 5088 Dihedral : 4.724 44.268 3926 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.17 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3602 helix: 0.24 (0.11), residues: 2300 sheet: -0.44 (0.76), residues: 52 loop : -1.96 (0.18), residues: 1250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 324 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 10 residues processed: 345 average time/residue: 0.4328 time to fit residues: 240.3897 Evaluate side-chains 295 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 285 time to evaluate : 3.659 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3364 time to fit residues: 10.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 4.9990 chunk 317 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 353 optimal weight: 0.6980 chunk 293 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2301 GLN ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29636 Z= 0.176 Angle : 0.622 16.648 40087 Z= 0.301 Chirality : 0.040 0.178 4569 Planarity : 0.004 0.042 5088 Dihedral : 4.587 45.648 3926 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.34 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3602 helix: 0.35 (0.11), residues: 2304 sheet: -0.46 (0.74), residues: 52 loop : -1.95 (0.18), residues: 1246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 300 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 317 average time/residue: 0.4445 time to fit residues: 227.8318 Evaluate side-chains 286 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 3.366 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3734 time to fit residues: 10.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 201 optimal weight: 0.5980 chunk 257 optimal weight: 0.0020 chunk 199 optimal weight: 10.0000 chunk 297 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 351 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 29636 Z= 0.157 Angle : 0.618 16.681 40087 Z= 0.297 Chirality : 0.040 0.207 4569 Planarity : 0.004 0.043 5088 Dihedral : 4.447 45.433 3926 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3602 helix: 0.47 (0.11), residues: 2296 sheet: -0.59 (0.72), residues: 54 loop : -1.88 (0.18), residues: 1252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 302 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 314 average time/residue: 0.4385 time to fit residues: 221.4596 Evaluate side-chains 277 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 268 time to evaluate : 3.631 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2798 time to fit residues: 9.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 223 optimal weight: 0.4980 chunk 239 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2807 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29636 Z= 0.178 Angle : 0.632 16.664 40087 Z= 0.303 Chirality : 0.040 0.287 4569 Planarity : 0.004 0.052 5088 Dihedral : 4.428 47.011 3926 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.56 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3602 helix: 0.50 (0.11), residues: 2304 sheet: -0.51 (0.72), residues: 54 loop : -1.89 (0.18), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 305 average time/residue: 0.4480 time to fit residues: 220.8993 Evaluate side-chains 286 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 270 time to evaluate : 3.561 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2917 time to fit residues: 13.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 0.0270 chunk 337 optimal weight: 0.9990 chunk 307 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 336 optimal weight: 9.9990 chunk 197 optimal weight: 0.0060 chunk 142 optimal weight: 0.0270 chunk 257 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 310 optimal weight: 0.0970 overall best weight: 0.1910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2543 ASN ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 29636 Z= 0.152 Angle : 0.636 16.687 40087 Z= 0.303 Chirality : 0.040 0.293 4569 Planarity : 0.004 0.053 5088 Dihedral : 4.350 45.427 3926 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3602 helix: 0.61 (0.11), residues: 2293 sheet: -0.51 (0.70), residues: 54 loop : -1.84 (0.18), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 295 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 300 average time/residue: 0.4347 time to fit residues: 212.6739 Evaluate side-chains 273 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 3.809 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4935 time to fit residues: 9.1424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 240 optimal weight: 0.8980 chunk 363 optimal weight: 1.9990 chunk 334 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN A1367 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1738 ASN ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 29636 Z= 0.191 Angle : 0.677 16.648 40087 Z= 0.320 Chirality : 0.041 0.291 4569 Planarity : 0.004 0.089 5088 Dihedral : 4.373 47.320 3926 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3602 helix: 0.55 (0.11), residues: 2304 sheet: -0.47 (0.72), residues: 54 loop : -1.85 (0.18), residues: 1244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 281 average time/residue: 0.4333 time to fit residues: 200.5747 Evaluate side-chains 273 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2855 time to fit residues: 7.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 0.0870 chunk 230 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 297 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.164946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.132137 restraints weight = 57806.935| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.61 r_work: 0.3712 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29636 Z= 0.163 Angle : 0.676 16.997 40087 Z= 0.318 Chirality : 0.041 0.291 4569 Planarity : 0.004 0.073 5088 Dihedral : 4.330 46.070 3926 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.98 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3602 helix: 0.56 (0.11), residues: 2303 sheet: -0.49 (0.70), residues: 54 loop : -1.82 (0.18), residues: 1245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6421.07 seconds wall clock time: 117 minutes 25.16 seconds (7045.16 seconds total)