Starting phenix.real_space_refine on Mon Nov 20 08:07:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfp_11185/11_2023/6zfp_11185.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= 0.001 sd= 0.012 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 193 5.16 5 C 18849 2.51 5 N 4964 2.21 5 O 5379 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 2585": "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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 29385 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3704, 29385 Classifications: {'peptide': 3704} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'CIS': 2, 'PTRANS': 161, 'TRANS': 3540} Chain breaks: 19 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'UNK:plan-1': 28, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Time building chain proxies: 15.08, per 1000 atoms: 0.51 Number of scatterers: 29385 At special positions: 0 Unit cell: (119.316, 144.092, 184.516, 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 193 16.00 O 5379 8.00 N 4964 7.00 C 18849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.73 Conformation dependent library (CDL) restraints added in 5.2 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7106 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 6 sheets defined 70.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.988A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 4.128A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 removed outlier: 4.100A pdb=" N VAL A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.649A pdb=" N ASP A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.847A 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: 4.209A 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: 4.321A pdb=" N SER A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.543A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 85 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.813A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.934A pdb=" N LYS A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.614A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.894A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.938A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.811A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 4.259A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 4.186A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.641A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.069A pdb=" N VAL A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.697A pdb=" N ASN A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.859A pdb=" N SER A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.857A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 450 through 469 removed outlier: 4.242A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.239A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.906A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.054A 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 638 through 644 removed outlier: 3.683A pdb=" N PHE A 641 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 643 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Proline residue: A 644 - end of helix Processing helix chain 'A' and resid 645 through 660 removed outlier: 4.155A pdb=" N GLN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.600A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 3.519A pdb=" N LYS A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 3.652A pdb=" N THR A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.925A pdb=" N LEU A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 760 removed outlier: 3.942A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) 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 762 through 780 removed outlier: 3.654A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 797 through 802 removed outlier: 3.675A pdb=" N THR A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 805 No H-bonds generated for 'chain 'A' and resid 803 through 805' Processing helix chain 'A' and resid 848 through 862 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.836A pdb=" N SER A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 921 removed outlier: 4.026A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 945 Processing helix chain 'A' and resid 958 through 974 removed outlier: 3.823A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.634A pdb=" N CYS A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 removed outlier: 3.574A pdb=" N ARG A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1023 through 1044 removed outlier: 3.634A 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) removed outlier: 3.580A pdb=" N ILE A1044 " --> pdb=" O SER A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1051 removed outlier: 4.155A pdb=" N GLU A1050 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.692A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) removed outlier: 3.671A 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) removed outlier: 3.510A pdb=" N TYR A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 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) Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1122 through 1141 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N LEU A1145 " --> pdb=" O LYS A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1180 through 1195 Processing helix chain 'A' and resid 1196 through 1198 No H-bonds generated for 'chain 'A' and resid 1196 through 1198' Processing helix chain 'A' and resid 1203 through 1215 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.548A pdb=" N ILE A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1272 removed outlier: 3.573A pdb=" N THR A1269 " --> pdb=" O GLU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.787A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 3.516A pdb=" N ALA A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1351 removed outlier: 3.704A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1361 removed outlier: 3.991A pdb=" N LEU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1360 " --> pdb=" O TRP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.179A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1390 through 1409 Proline residue: A1396 - end of helix removed outlier: 3.772A 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 1411 through 1421 Processing helix chain 'A' and resid 1424 through 1433 removed outlier: 3.588A pdb=" N CYS A1432 " --> pdb=" O ILE A1428 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1433 " --> pdb=" O GLU A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1476 through 1481 Processing helix chain 'A' and resid 1481 through 1486 Processing helix chain 'A' and resid 1506 through 1520 Processing helix chain 'A' and resid 1524 through 1533 removed outlier: 3.620A pdb=" N SER A1530 " --> pdb=" O GLU A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.716A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 4.403A 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 1574 through 1585 removed outlier: 4.402A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 removed outlier: 3.813A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 3.670A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1630 removed outlier: 3.501A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.795A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1680 removed outlier: 3.615A pdb=" N VAL A1671 " --> pdb=" O SER A1667 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1693 Processing helix chain 'A' and resid 1695 through 1700 removed outlier: 3.851A pdb=" N PHE A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1722 removed outlier: 3.808A pdb=" N LEU A1710 " --> pdb=" O SER A1706 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1754 Processing helix chain 'A' and resid 1755 through 1767 Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1790 through 1806 Processing helix chain 'A' and resid 1813 through 1822 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: 4.071A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 3.650A pdb=" N GLU A1838 " --> pdb=" O ASP A1834 " (cutoff:3.500A) removed outlier: 4.608A 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: 3.861A 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) removed outlier: 3.574A pdb=" N LEU A1851 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1863 through 1882 Processing helix chain 'A' and resid 1885 through 1890 removed outlier: 3.728A pdb=" N VAL A1889 " --> pdb=" O PRO A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 3.679A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A1923 " --> pdb=" O CYS A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 removed outlier: 3.578A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1970 through 1975 removed outlier: 3.892A pdb=" N ASN A1974 " --> pdb=" O LYS A1970 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A1975 " --> pdb=" O PRO A1971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1970 through 1975' Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.882A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2135 removed outlier: 3.626A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A2132 " --> pdb=" O PHE A2128 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.606A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.811A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2153 through 2158' Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 5.038A pdb=" N SER A2166 " --> pdb=" O LYS A2162 " (cutoff:3.500A) Proline residue: A2167 - end of helix Processing helix chain 'A' and resid 2183 through 2196 removed outlier: 3.580A pdb=" N TRP A2196 " --> pdb=" O THR A2192 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 4.009A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 removed outlier: 3.514A pdb=" N LYS A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A2260 " --> pdb=" O ILE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2267 through 2269 No H-bonds generated for 'chain 'A' and resid 2267 through 2269' Processing helix chain 'A' and resid 2270 through 2283 removed outlier: 3.532A pdb=" N MET A2281 " --> pdb=" O LEU A2277 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 removed outlier: 4.268A pdb=" N TYR A2299 " --> pdb=" O GLN A2295 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2309 Processing helix chain 'A' and resid 2312 through 2333 removed outlier: 4.007A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A2319 " --> pdb=" O VAL A2315 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 4.188A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2370 removed outlier: 3.718A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2375 removed outlier: 3.938A pdb=" N LEU A2374 " --> pdb=" O PHE A2371 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2386 Processing helix chain 'A' and resid 2387 through 2389 No H-bonds generated for 'chain 'A' and resid 2387 through 2389' Processing helix chain 'A' and resid 2391 through 2404 removed outlier: 3.941A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A2404 " --> pdb=" O VAL A2400 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 3.712A pdb=" N VAL A2423 " --> pdb=" O ASP A2419 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2419 through 2424' Processing helix chain 'A' and resid 2429 through 2443 removed outlier: 3.598A pdb=" N CYS A2435 " --> pdb=" O ARG A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2446 No H-bonds generated for 'chain 'A' and resid 2444 through 2446' Processing helix chain 'A' and resid 2447 through 2459 removed outlier: 3.925A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix Processing helix chain 'A' and resid 2460 through 2462 No H-bonds generated for 'chain 'A' and resid 2460 through 2462' Processing helix chain 'A' and resid 2469 through 2484 removed outlier: 3.730A pdb=" N ASN A2475 " --> pdb=" O GLU A2471 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.775A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2512 No H-bonds generated for 'chain 'A' and resid 2510 through 2512' Processing helix chain 'A' and resid 2514 through 2526 Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2543 through 2546 Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2787 through 2799 Proline residue: A2793 - end of helix Processing helix chain 'A' and resid 2801 through 2820 Processing helix chain 'A' and resid 2825 through 2846 Processing helix chain 'A' and resid 2851 through 2864 removed outlier: 3.659A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2871 removed outlier: 4.237A pdb=" N SER A2870 " --> pdb=" O ALA A2867 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2883 Processing helix chain 'A' and resid 2885 through 2900 removed outlier: 3.678A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A2898 " --> pdb=" O GLU A2894 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A2900 " --> pdb=" O ALA A2896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2933 removed outlier: 3.579A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.525A pdb=" N GLY A2941 " --> pdb=" O ASP A2937 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A2945 " --> pdb=" O GLY A2941 " (cutoff:3.500A) Processing helix chain 'A' and resid 2954 through 2962 removed outlier: 3.546A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.649A pdb=" N ASN A2977 " --> pdb=" O ASP A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 removed outlier: 4.423A 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 3007 through 3014 removed outlier: 3.596A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3054 removed outlier: 3.504A pdb=" N SER A3047 " --> pdb=" O TYR A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3071 removed outlier: 4.269A pdb=" N GLY A3071 " --> pdb=" O LYS A3067 " (cutoff:3.500A) Processing helix chain 'A' and resid 3074 through 3081 removed outlier: 3.689A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3082 through 3094 removed outlier: 3.705A pdb=" N LEU A3092 " --> pdb=" O LEU A3088 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3117 removed outlier: 3.546A pdb=" N ALA A3099 " --> pdb=" O ASP A3095 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A3116 " --> pdb=" O GLN A3112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A3117 " --> pdb=" O ASN A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3121 through 3131 removed outlier: 3.568A pdb=" N THR A3127 " --> pdb=" O GLN A3123 " (cutoff:3.500A) removed outlier: 3.963A 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) Processing helix chain 'A' and resid 3132 through 3146 removed outlier: 3.952A pdb=" N ILE A3138 " --> pdb=" O ALA A3134 " (cutoff:3.500A) removed outlier: 3.944A 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 3153 through 3167 removed outlier: 4.240A pdb=" N LEU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A3167 " --> pdb=" O THR A3163 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.787A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A3184 " --> pdb=" O ASP A3180 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A3195 " --> pdb=" O SER A3191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A3196 " --> pdb=" O LYS A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.744A pdb=" N CYS A3234 " --> pdb=" O LEU A3230 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3253 through 3262 Processing helix chain 'A' and resid 3271 through 3287 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 3290 through 3307 removed outlier: 4.577A pdb=" N GLU A3295 " --> pdb=" O GLN A3291 " (cutoff:3.500A) removed outlier: 5.309A 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 3322 through 3344 removed outlier: 3.720A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3345 through 3353 removed outlier: 4.037A pdb=" N LEU A3348 " --> pdb=" O PRO A3345 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU A3350 " --> pdb=" O CYS A3347 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU A3353 " --> pdb=" O GLU A3350 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3364 removed outlier: 3.983A pdb=" N ILE A3359 " --> pdb=" O LYS A3355 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A3360 " --> pdb=" O ALA A3356 " (cutoff:3.500A) Processing helix chain 'A' and resid 3369 through 3392 Processing helix chain 'A' and resid 3406 through 3430 removed outlier: 3.785A pdb=" N ILE A3410 " --> pdb=" O ALA A3406 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A3430 " --> pdb=" O LYS A3426 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.810A pdb=" N LEU A3445 " --> pdb=" O ALA A3441 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3464 removed outlier: 3.605A pdb=" N LYS A3464 " --> pdb=" O GLU A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3472 removed outlier: 3.823A 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 3475 through 3480 removed outlier: 3.733A pdb=" N GLU A3478 " --> pdb=" O TYR A3475 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A3480 " --> pdb=" O GLU A3477 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3488 removed outlier: 3.545A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3497 No H-bonds generated for 'chain 'A' and resid 3495 through 3497' Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3504 through 3506 No H-bonds generated for 'chain 'A' and resid 3504 through 3506' Processing helix chain 'A' and resid 3514 through 3525 removed outlier: 3.537A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3538 removed outlier: 3.911A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) Processing helix chain 'A' and resid 3548 through 3563 removed outlier: 4.093A pdb=" N GLU A3553 " --> pdb=" O HIS A3549 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE A3554 " --> pdb=" O LYS A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3577 removed outlier: 3.647A pdb=" N GLN A3577 " --> pdb=" O ASN A3573 " (cutoff:3.500A) Processing helix chain 'A' and resid 3580 through 3594 Processing helix chain 'A' and resid 3605 through 3607 No H-bonds generated for 'chain 'A' and resid 3605 through 3607' Processing helix chain 'A' and resid 3608 through 3617 removed outlier: 3.526A pdb=" N ALA A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 removed outlier: 3.688A pdb=" N PHE A3632 " --> pdb=" O PHE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3649 through 3653 Processing helix chain 'A' and resid 3657 through 3671 removed outlier: 3.623A pdb=" N ASP A3661 " --> pdb=" O SER A3657 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3672 through 3674 No H-bonds generated for 'chain 'A' and resid 3672 through 3674' Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3777 Processing helix chain 'A' and resid 3779 through 3784 removed outlier: 3.740A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3819 removed outlier: 3.586A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3846 removed outlier: 4.063A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 4.015A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3865 through 3876 removed outlier: 3.654A pdb=" N SER A3876 " --> pdb=" O ARG A3872 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3890 removed outlier: 3.750A pdb=" N ARG A3885 " --> pdb=" O ASP A3881 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A3890 " --> pdb=" O ALA A3886 " (cutoff:3.500A) Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 3.995A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.514A 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 3924 through 3926 No H-bonds generated for 'chain 'A' and resid 3924 through 3926' Processing helix chain 'A' and resid 3947 through 3952 Processing helix chain 'A' and resid 3964 through 3969 Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.609A 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) removed outlier: 4.160A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3994 through 4007 removed outlier: 4.613A pdb=" N LEU A3998 " --> pdb=" O ASP A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4022 removed outlier: 3.680A pdb=" N LYS A4022 " --> pdb=" O GLN A4018 " (cutoff:3.500A) Processing helix chain 'A' and resid 4043 through 4050 removed outlier: 3.855A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 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 4073 through 4082 Processing helix chain 'A' and resid 4101 through 4112 removed outlier: 3.663A pdb=" N LEU A4107 " --> pdb=" O GLN A4103 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 5010 through 5015 removed outlier: 3.681A pdb=" N UNK A5013 " --> pdb=" O UNK A5010 " (cutoff:3.500A) Processing helix chain 'A' and resid 6002 through 6010 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) Processing sheet with id=AA1, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA2, first strand: chain 'A' and resid 893 through 895 Processing sheet with id=AA3, first strand: chain 'A' and resid 2586 through 2587 Processing sheet with id=AA4, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.796A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A3727 " --> pdb=" O ARG A3737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.796A pdb=" N GLY A3721 " --> pdb=" O ARG A3741 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A3746 " --> pdb=" O GLY A3742 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1487 hydrogen bonds defined for protein. 4368 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: 14.93 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5314 1.32 - 1.45: 7217 1.45 - 1.57: 17154 1.57 - 1.69: 0 1.69 - 1.81: 301 Bond restraints: 29986 Sorted by residual: bond pdb=" C THR A3484 " pdb=" O THR A3484 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.16e-02 7.43e+03 7.46e+00 bond pdb=" N SER A3481 " pdb=" CA SER A3481 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.02e+00 bond pdb=" C LEU A3482 " pdb=" O LEU A3482 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.26e-02 6.30e+03 6.85e+00 bond pdb=" C LEU A3480 " pdb=" O LEU A3480 " ideal model delta sigma weight residual 1.235 1.204 0.032 1.26e-02 6.30e+03 6.26e+00 bond pdb=" N LEU A3482 " pdb=" CA LEU A3482 " ideal model delta sigma weight residual 1.457 1.426 0.032 1.29e-02 6.01e+03 6.08e+00 ... (remaining 29981 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.82: 551 104.82 - 112.18: 14974 112.18 - 119.53: 10395 119.53 - 126.89: 14286 126.89 - 134.24: 350 Bond angle restraints: 40556 Sorted by residual: 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 7.12e+01 angle pdb=" N GLN A3074 " pdb=" CA GLN A3074 " pdb=" C GLN A3074 " ideal model delta sigma weight residual 114.04 107.90 6.14 1.24e+00 6.50e-01 2.45e+01 angle pdb=" N ILE A3487 " pdb=" CA ILE A3487 " pdb=" C ILE A3487 " ideal model delta sigma weight residual 112.04 117.62 -5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" N ILE A1013 " pdb=" CA ILE A1013 " pdb=" C ILE A1013 " ideal model delta sigma weight residual 112.96 109.18 3.78 1.00e+00 1.00e+00 1.43e+01 angle pdb=" C ASN A4088 " pdb=" N ILE A4089 " pdb=" CA ILE A4089 " ideal model delta sigma weight residual 121.65 118.33 3.32 9.40e-01 1.13e+00 1.24e+01 ... (remaining 40551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 16352 17.62 - 35.25: 1597 35.25 - 52.87: 276 52.87 - 70.50: 45 70.50 - 88.12: 22 Dihedral angle restraints: 18292 sinusoidal: 7392 harmonic: 10900 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 180.00 154.83 25.17 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 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 18289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4380 0.089 - 0.178: 237 0.178 - 0.267: 4 0.267 - 0.356: 0 0.356 - 0.445: 1 Chirality restraints: 4622 Sorted by residual: 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 4.96e+00 chirality pdb=" CA LEU A1966 " pdb=" N LEU A1966 " pdb=" C LEU A1966 " pdb=" CB LEU A1966 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG A1811 " pdb=" N ARG A1811 " pdb=" C ARG A1811 " pdb=" CB ARG A1811 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 4619 not shown) Planarity restraints: 5151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1409 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A1410 " 0.092 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 delta sigma weight rms_deltas residual plane pdb=" C PHE A2851 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO A2852 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2852 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2852 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2371 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A2372 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A2372 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2372 " -0.026 5.00e-02 4.00e+02 ... (remaining 5148 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3272 2.74 - 3.28: 31141 3.28 - 3.82: 47529 3.82 - 4.36: 56577 4.36 - 4.90: 95913 Nonbonded interactions: 234432 Sorted by model distance: nonbonded pdb=" O GLU A 203 " pdb=" OG1 THR A 206 " model vdw 2.198 2.440 nonbonded pdb=" O SER A3288 " pdb=" NH1 ARG A3289 " model vdw 2.199 2.520 nonbonded pdb=" O ALA A2796 " pdb=" NH1 ARG A2800 " model vdw 2.208 2.520 nonbonded pdb=" O LEU A3011 " pdb=" OG1 THR A3016 " model vdw 2.213 2.440 nonbonded pdb=" O PHE A1819 " pdb=" OG SER A1823 " model vdw 2.217 2.440 ... (remaining 234427 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: 3.940 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: 17.870 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 81.100 Find NCS groups from input model: 0.810 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.006 0.058 29986 Z= 0.370 Angle : 0.702 10.123 40556 Z= 0.378 Chirality : 0.045 0.445 4622 Planarity : 0.004 0.053 5151 Dihedral : 14.338 88.119 11186 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.54 % Rotamer: Outliers : 0.12 % Allowed : 0.28 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3640 helix: -0.04 (0.11), residues: 2316 sheet: -0.77 (0.66), residues: 52 loop : -2.13 (0.18), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 239 time to evaluate : 3.357 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 242 average time/residue: 0.4211 time to fit residues: 167.6094 Evaluate side-chains 200 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 3.283 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2805 time to fit residues: 5.0430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 189 optimal weight: 0.0470 chunk 149 optimal weight: 0.8980 chunk 290 optimal weight: 0.0870 chunk 112 optimal weight: 8.9990 chunk 176 optimal weight: 0.2980 chunk 215 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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** A1374 GLN A1477 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 ASN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3501 HIS ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3580 ASN A3643 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29986 Z= 0.158 Angle : 0.582 9.904 40556 Z= 0.294 Chirality : 0.040 0.173 4622 Planarity : 0.004 0.049 5151 Dihedral : 4.861 27.336 3969 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 0.34 % Allowed : 6.62 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3640 helix: 0.44 (0.11), residues: 2353 sheet: -0.41 (0.69), residues: 52 loop : -1.96 (0.18), residues: 1235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 249 average time/residue: 0.4702 time to fit residues: 193.1010 Evaluate side-chains 210 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 3.500 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3602 time to fit residues: 8.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 0.0980 chunk 104 optimal weight: 0.0770 chunk 279 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 336 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 299 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 925 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3951 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29986 Z= 0.182 Angle : 0.557 9.660 40556 Z= 0.279 Chirality : 0.039 0.164 4622 Planarity : 0.004 0.048 5151 Dihedral : 4.599 26.205 3969 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 0.71 % Allowed : 9.31 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.35 (0.15), residues: 3640 helix: 0.64 (0.11), residues: 2326 sheet: -0.39 (0.67), residues: 52 loop : -1.85 (0.18), residues: 1262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 229 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 246 average time/residue: 0.4235 time to fit residues: 173.4505 Evaluate side-chains 211 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2911 time to fit residues: 8.7000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 226 optimal weight: 0.0020 chunk 337 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- 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** A1477 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1738 ASN ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29986 Z= 0.270 Angle : 0.585 10.033 40556 Z= 0.292 Chirality : 0.041 0.239 4622 Planarity : 0.004 0.050 5151 Dihedral : 4.618 25.875 3969 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.23 % Favored : 92.66 % Rotamer: Outliers : 1.11 % Allowed : 11.19 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.36 (0.15), residues: 3640 helix: 0.64 (0.11), residues: 2350 sheet: -0.39 (0.67), residues: 52 loop : -1.94 (0.18), residues: 1238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 242 average time/residue: 0.4162 time to fit residues: 168.8086 Evaluate side-chains 217 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 3.788 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2838 time to fit residues: 13.1426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 2.9990 chunk 203 optimal weight: 0.0470 chunk 5 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 305 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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** A1477 HIS ** A1574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29986 Z= 0.180 Angle : 0.559 10.752 40556 Z= 0.277 Chirality : 0.039 0.192 4622 Planarity : 0.004 0.047 5151 Dihedral : 4.480 26.493 3969 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.65 % Favored : 93.24 % Rotamer: Outliers : 0.49 % Allowed : 12.12 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.21 (0.15), residues: 3640 helix: 0.73 (0.11), residues: 2359 sheet: -0.30 (0.68), residues: 52 loop : -1.85 (0.18), residues: 1229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 239 average time/residue: 0.4860 time to fit residues: 192.6016 Evaluate side-chains 207 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3221 time to fit residues: 8.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.0970 chunk 322 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 357 optimal weight: 20.0000 chunk 297 optimal weight: 3.9990 chunk 165 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** A1614 GLN A2351 GLN A2365 ASN A2865 HIS ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29986 Z= 0.140 Angle : 0.550 11.727 40556 Z= 0.271 Chirality : 0.038 0.176 4622 Planarity : 0.004 0.045 5151 Dihedral : 4.299 26.784 3969 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.68 % Rotamer: Outliers : 0.68 % Allowed : 12.96 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.05 (0.15), residues: 3640 helix: 0.96 (0.12), residues: 2319 sheet: -0.27 (0.69), residues: 52 loop : -1.70 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 243 average time/residue: 0.4540 time to fit residues: 179.2672 Evaluate side-chains 205 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 3.830 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2994 time to fit residues: 7.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 0.0970 chunk 261 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 356 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** A2865 HIS ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29986 Z= 0.171 Angle : 0.556 10.957 40556 Z= 0.273 Chirality : 0.039 0.196 4622 Planarity : 0.004 0.046 5151 Dihedral : 4.254 26.124 3969 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 0.65 % Allowed : 13.45 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.06 (0.15), residues: 3640 helix: 0.99 (0.12), residues: 2330 sheet: -0.20 (0.69), residues: 52 loop : -1.76 (0.18), residues: 1258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 227 average time/residue: 0.4526 time to fit residues: 171.6595 Evaluate side-chains 212 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3078 time to fit residues: 8.1402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29986 Z= 0.224 Angle : 0.575 10.493 40556 Z= 0.283 Chirality : 0.040 0.167 4622 Planarity : 0.004 0.048 5151 Dihedral : 4.317 25.818 3969 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 0.37 % Allowed : 13.95 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.07 (0.15), residues: 3640 helix: 1.00 (0.11), residues: 2327 sheet: -0.42 (0.65), residues: 58 loop : -1.76 (0.18), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 221 average time/residue: 0.4572 time to fit residues: 168.0074 Evaluate side-chains 209 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 3.704 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2709 time to fit residues: 6.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 0.0020 chunk 341 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 332 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 331 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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** A2865 HIS ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29986 Z= 0.151 Angle : 0.565 10.920 40556 Z= 0.277 Chirality : 0.039 0.215 4622 Planarity : 0.004 0.045 5151 Dihedral : 4.222 26.455 3969 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 0.25 % Allowed : 14.44 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3640 helix: 1.10 (0.11), residues: 2321 sheet: -0.33 (0.66), residues: 58 loop : -1.74 (0.18), residues: 1261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 222 average time/residue: 0.4404 time to fit residues: 162.2158 Evaluate side-chains 216 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3352 time to fit residues: 8.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 226 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.1244 ------------------------------------------------------------------------------- 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** A1687 HIS A2865 HIS ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29986 Z= 0.171 Angle : 0.577 10.764 40556 Z= 0.281 Chirality : 0.039 0.199 4622 Planarity : 0.004 0.046 5151 Dihedral : 4.182 26.138 3969 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 0.12 % Allowed : 14.66 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.23 (0.15), residues: 3640 helix: 1.13 (0.11), residues: 2328 sheet: -0.33 (0.65), residues: 58 loop : -1.72 (0.18), residues: 1254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.4472 time to fit residues: 168.4756 Evaluate side-chains 215 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 0.8980 chunk 312 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 293 optimal weight: 4.9990 chunk 123 optimal weight: 0.0000 chunk 301 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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** A1687 HIS A2865 HIS ** A3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.102085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075910 restraints weight = 66934.842| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.50 r_work: 0.3069 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29986 Z= 0.145 Angle : 0.563 10.996 40556 Z= 0.276 Chirality : 0.039 0.193 4622 Planarity : 0.004 0.045 5151 Dihedral : 4.080 26.209 3969 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 0.15 % Allowed : 14.84 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: 0.31 (0.15), residues: 3640 helix: 1.22 (0.12), residues: 2324 sheet: -0.32 (0.66), residues: 58 loop : -1.72 (0.18), residues: 1258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6442.05 seconds wall clock time: 117 minutes 31.03 seconds (7051.03 seconds total)