Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 17:08:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh4_11213/10_2023/6zh4_11213.pdb" } resolution = 3.62 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= 0.010 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 18827 2.51 5 N 4960 2.21 5 O 5372 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 ARG 142": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 775": "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 GLU 985": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A GLU 1182": "OE1" <-> "OE2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A ARG 1245": "NH1" <-> "NH2" Residue "A ARG 1321": "NH1" <-> "NH2" Residue "A GLU 1328": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A GLU 1430": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A GLU 1516": "OE1" <-> "OE2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A GLU 1728": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1837": "NH1" <-> "NH2" Residue "A GLU 1838": "OE1" <-> "OE2" Residue "A ARG 1854": "NH1" <-> "NH2" Residue "A GLU 1893": "OE1" <-> "OE2" Residue "A GLU 1925": "OE1" <-> "OE2" Residue "A GLU 1935": "OE1" <-> "OE2" Residue "A ARG 1937": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A GLU 1969": "OE1" <-> "OE2" Residue "A GLU 1979": "OE1" <-> "OE2" Residue "A GLU 2087": "OE1" <-> "OE2" 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 GLU 2180": "OE1" <-> "OE2" Residue "A GLU 2209": "OE1" <-> "OE2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A GLU 2258": "OE1" <-> "OE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A GLU 2450": "OE1" <-> "OE2" Residue "A GLU 2471": "OE1" <-> "OE2" Residue "A GLU 2894": "OE1" <-> "OE2" Residue "A GLU 2895": "OE1" <-> "OE2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2922": "NH1" <-> "NH2" Residue "A GLU 3072": "OE1" <-> "OE2" Residue "A GLU 3140": "OE1" <-> "OE2" Residue "A ARG 3282": "NH1" <-> "NH2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3350": "OE1" <-> "OE2" Residue "A GLU 3352": "OE1" <-> "OE2" Residue "A ARG 3357": "NH1" <-> "NH2" Residue "A ARG 3358": "NH1" <-> "NH2" Residue "A ARG 3380": "NH1" <-> "NH2" Residue "A GLU 3395": "OE1" <-> "OE2" Residue "A ARG 3425": "NH1" <-> "NH2" Residue "A GLU 3473": "OE1" <-> "OE2" Residue "A GLU 3519": "OE1" <-> "OE2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A PHE 3690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3700": "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 ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A GLU 3895": "OE1" <-> "OE2" Residue "A GLU 3933": "OE1" <-> "OE2" Residue "A GLU 4017": "OE1" <-> "OE2" Residue "A GLU 4030": "OE1" <-> "OE2" Residue "A ARG 4082": "NH1" <-> "NH2" Residue "A GLU 4100": "OE1" <-> "OE2" Residue "A ARG 4119": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 29352 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 29352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3698, 29352 Classifications: {'peptide': 3698} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'CIS': 2, 'PTRANS': 161, 'TRANS': 3534} Chain breaks: 20 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'UNK:plan-1': 28, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 133 Time building chain proxies: 15.26, per 1000 atoms: 0.52 Number of scatterers: 29352 At special positions: 0 Unit cell: (121.924, 145.396, 183.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 193 16.00 O 5372 8.00 N 4960 7.00 C 18827 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: 10.80 Conformation dependent library (CDL) restraints added in 4.1 seconds 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 6 sheets defined 70.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.980A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.674A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.923A pdb=" N GLN A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.724A pdb=" N PHE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 60 through 69 removed outlier: 4.214A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.912A pdb=" N ARG A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.582A pdb=" N ASN A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 118 No H-bonds generated for 'chain 'A' and resid 117 through 118' Processing helix chain 'A' and resid 127 through 128 No H-bonds generated for 'chain 'A' and resid 127 through 128' Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.631A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.090A pdb=" N TYR A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 173 through 185 removed outlier: 4.373A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.935A pdb=" N CYS A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 4.000A pdb=" N THR A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.752A 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 303 removed outlier: 3.542A pdb=" N ASP A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 379 through 397 removed outlier: 4.433A pdb=" N PHE A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 422 removed outlier: 3.732A pdb=" N VAL A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 431 through 445 removed outlier: 3.575A pdb=" N LEU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.890A pdb=" N LEU A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 492 removed outlier: 4.392A pdb=" N ARG A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 539 through 547 removed outlier: 4.087A pdb=" N SER A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.871A pdb=" N PHE A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.849A pdb=" N PHE A 641 " --> pdb=" O GLN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.820A pdb=" N SER A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 656 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.526A pdb=" N LYS A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 672 " --> pdb=" O LYS A 668 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 679 " --> pdb=" O ARG A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 718 removed outlier: 4.145A pdb=" N VAL A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 735 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.768A pdb=" N GLU A 742 " --> pdb=" O HIS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 758 removed outlier: 3.783A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 762 through 780 removed outlier: 3.567A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.888A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.811A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 946 removed outlier: 3.655A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 Proline residue: A 967 - end of helix Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1015 Processing helix chain 'A' and resid 1023 through 1044 removed outlier: 3.513A pdb=" N ASP A1027 " --> pdb=" O SER A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1050 removed outlier: 3.504A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A1050 " --> pdb=" O PRO A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1045 through 1050' Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1083 removed outlier: 3.804A pdb=" N ARG A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1114 removed outlier: 3.736A pdb=" N VAL A1100 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 5.604A 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 removed outlier: 3.631A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (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: 3.752A pdb=" N GLU A1225 " --> pdb=" O ILE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1251 through 1273 Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 3.625A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 Processing helix chain 'A' and resid 1323 through 1351 removed outlier: 4.005A pdb=" N GLY A1327 " --> pdb=" O SER A1323 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A1328 " --> pdb=" O PRO A1324 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A1329 " --> pdb=" O GLN A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1361 Processing helix chain 'A' and resid 1364 through 1378 removed outlier: 4.220A pdb=" N ARG A1370 " --> pdb=" O THR A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 removed outlier: 3.825A pdb=" N ILE A1382 " --> pdb=" O GLU A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1409 removed outlier: 4.056A pdb=" N VAL A1398 " --> pdb=" O HIS A1394 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.553A pdb=" N LEU A1415 " --> pdb=" O TYR A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1434 removed outlier: 3.967A pdb=" N ILE A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A1429 " --> pdb=" O ALA A1425 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.517A pdb=" N ALA A1449 " --> pdb=" O ARG A1445 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1472 through 1475 Processing helix chain 'A' and resid 1476 through 1485 removed outlier: 3.545A pdb=" N GLY A1480 " --> pdb=" O HIS A1476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A1481 " --> pdb=" O HIS A1477 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1484 " --> pdb=" O GLY A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.831A pdb=" N ILE A1491 " --> pdb=" O TYR A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1521 removed outlier: 3.994A pdb=" N PHE A1521 " --> pdb=" O LEU A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1533 Processing helix chain 'A' and resid 1555 through 1563 Processing helix chain 'A' and resid 1563 through 1574 removed outlier: 3.502A pdb=" N ILE A1567 " --> pdb=" O PHE A1563 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A1568 " --> pdb=" O SER A1564 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1585 removed outlier: 3.915A pdb=" N LEU A1580 " --> pdb=" O ASP A1576 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1607 Processing helix chain 'A' and resid 1611 through 1625 removed outlier: 3.524A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1633 removed outlier: 3.710A pdb=" N ASP A1630 " --> pdb=" O LYS A1627 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A1631 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 3.741A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 3.629A pdb=" N LYS A1689 " --> pdb=" O ASP A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 Processing helix chain 'A' and resid 1706 through 1722 Processing helix chain 'A' and resid 1733 through 1754 removed outlier: 3.509A pdb=" N ASP A1748 " --> pdb=" O LYS A1744 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A1752 " --> pdb=" O ASP A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1768 removed outlier: 3.595A pdb=" N ARG A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1786 removed outlier: 3.704A pdb=" N PHE A1778 " --> pdb=" O MET A1774 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A1779 " --> pdb=" O GLU A1775 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1784 " --> pdb=" O SER A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 Processing helix chain 'A' and resid 1813 through 1823 removed outlier: 3.592A pdb=" N SER A1818 " --> pdb=" O PHE A1814 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1831 removed outlier: 3.529A pdb=" N LEU A1827 " --> pdb=" O SER A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1853 removed outlier: 4.679A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A1853 " --> pdb=" O ASP A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1862 through 1882 removed outlier: 3.901A pdb=" N GLN A1866 " --> pdb=" O THR A1862 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A1882 " --> pdb=" O ASP A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 4.248A pdb=" N ALA A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1956 removed outlier: 3.952A pdb=" N CYS A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A1956 " --> pdb=" O ILE A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2106 removed outlier: 3.752A pdb=" N ARG A2106 " --> pdb=" O LYS A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2135 removed outlier: 3.718A pdb=" N PHE A2128 " --> pdb=" O SER A2124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A2129 " --> pdb=" O TRP A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2153 Processing helix chain 'A' and resid 2153 through 2158 removed outlier: 3.611A pdb=" N PHE A2157 " --> pdb=" O THR A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2160 through 2172 removed outlier: 4.872A 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: 3.637A pdb=" N SER A2195 " --> pdb=" O ALA A2191 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 removed outlier: 3.957A pdb=" N GLU A2209 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A2222 " --> pdb=" O PHE A2218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2245 Processing helix chain 'A' and resid 2254 through 2261 removed outlier: 3.950A pdb=" N GLU A2258 " --> pdb=" O ARG A2254 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2283 removed outlier: 3.683A pdb=" N VAL A2272 " --> pdb=" O LYS A2268 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY A2273 " --> pdb=" O ASP A2269 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2305 removed outlier: 3.691A 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 2330 removed outlier: 4.178A pdb=" N TYR A2316 " --> pdb=" O TYR A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2354 removed outlier: 3.539A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2369 removed outlier: 3.617A pdb=" N ILE A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2374 through 2377 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 2403 removed outlier: 3.983A pdb=" N VAL A2400 " --> pdb=" O LEU A2396 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A2401 " --> pdb=" O CYS A2397 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2418 removed outlier: 3.513A pdb=" N SER A2417 " --> pdb=" O PHE A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2419 through 2424 removed outlier: 4.217A pdb=" N MET A2424 " --> pdb=" O PHE A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2441 removed outlier: 3.614A pdb=" N VAL A2434 " --> pdb=" O GLU A2430 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS A2435 " --> pdb=" O ARG A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2442 through 2446 Processing helix chain 'A' and resid 2447 through 2460 removed outlier: 3.875A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 3.762A pdb=" N GLU A2460 " --> pdb=" O ASN A2456 " (cutoff:3.500A) Processing helix chain 'A' and resid 2468 through 2484 removed outlier: 3.648A pdb=" N GLN A2472 " --> pdb=" O THR A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2509 removed outlier: 3.511A pdb=" N GLN A2508 " --> pdb=" O ASP A2504 " (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 2527 Processing helix chain 'A' and resid 2534 through 2543 removed outlier: 3.866A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2546 No H-bonds generated for 'chain 'A' and resid 2544 through 2546' Processing helix chain 'A' and resid 2557 through 2564 Processing helix chain 'A' and resid 2565 through 2569 Processing helix chain 'A' and resid 2786 through 2789 Processing helix chain 'A' and resid 2790 through 2799 Processing helix chain 'A' and resid 2801 through 2821 removed outlier: 3.745A pdb=" N ASP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) Processing helix chain 'A' and resid 2826 through 2842 Processing helix chain 'A' and resid 2851 through 2865 removed outlier: 3.782A pdb=" N GLN A2864 " --> pdb=" O ASP A2860 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A2865 " --> pdb=" O ILE A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2882 removed outlier: 3.912A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2899 removed outlier: 3.693A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2933 Processing helix chain 'A' and resid 2935 through 2946 removed outlier: 3.711A pdb=" N LEU A2939 " --> pdb=" O GLU A2935 " (cutoff:3.500A) Processing helix chain 'A' and resid 2950 through 2962 removed outlier: 3.710A pdb=" N GLN A2954 " --> pdb=" O LYS A2950 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A2962 " --> pdb=" O LEU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2964 through 2977 removed outlier: 3.623A pdb=" N ALA A2968 " --> pdb=" O ASP A2964 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A2970 " --> pdb=" O SER A2966 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A2971 " --> pdb=" O GLU A2967 " (cutoff:3.500A) Processing helix chain 'A' and resid 2987 through 3005 Processing helix chain 'A' and resid 3007 through 3014 removed outlier: 3.830A pdb=" N CYS A3014 " --> pdb=" O SER A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3027 through 3032 removed outlier: 4.311A pdb=" N SER A3032 " --> pdb=" O ASN A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3040 through 3054 Processing helix chain 'A' and resid 3059 through 3069 Processing helix chain 'A' and resid 3075 through 3080 Processing helix chain 'A' and resid 3082 through 3093 Processing helix chain 'A' and resid 3097 through 3117 Processing helix chain 'A' and resid 3121 through 3131 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 4.050A pdb=" N LEU A3135 " --> pdb=" O SER A3131 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A3139 " --> pdb=" O LEU A3135 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3166 removed outlier: 3.842A pdb=" N THR A3163 " --> pdb=" O ARG A3159 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3196 removed outlier: 3.724A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A3180 " --> pdb=" O MET A3176 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP A3181 " --> pdb=" O ASN A3177 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG A3186 " --> pdb=" O ILE A3182 " (cutoff:3.500A) Processing helix chain 'A' and resid 3230 through 3249 removed outlier: 3.777A pdb=" N PHE A3236 " --> pdb=" O ARG A3232 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A3243 " --> pdb=" O LYS A3239 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3261 Processing helix chain 'A' and resid 3262 through 3266 Processing helix chain 'A' and resid 3270 through 3287 removed outlier: 3.740A pdb=" N VAL A3274 " --> pdb=" O ASP A3270 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3306 removed outlier: 3.905A pdb=" N VAL A3300 " --> pdb=" O GLN A3296 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A3301 " --> pdb=" O VAL A3297 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A3302 " --> pdb=" O LEU A3298 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A3303 " --> pdb=" O THR A3299 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3344 removed outlier: 3.968A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A3344 " --> pdb=" O ALA A3340 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3364 Processing helix chain 'A' and resid 3369 through 3392 removed outlier: 3.716A pdb=" N ALA A3375 " --> pdb=" O GLU A3371 " (cutoff:3.500A) Processing helix chain 'A' and resid 3406 through 3430 removed outlier: 3.542A pdb=" N ILE A3410 " --> pdb=" O ALA A3406 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A3423 " --> pdb=" O PHE A3419 " (cutoff:3.500A) Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.808A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3458 through 3470 Proline residue: A3466 - end of helix removed outlier: 3.825A pdb=" N LEU A3469 " --> pdb=" O PHE A3465 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3488 removed outlier: 4.162A pdb=" N SER A3488 " --> pdb=" O THR A3484 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 3529 through 3540 removed outlier: 3.985A pdb=" N GLU A3538 " --> pdb=" O ILE A3534 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A3539 " --> pdb=" O ILE A3535 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3563 removed outlier: 3.795A pdb=" N ASP A3563 " --> pdb=" O LYS A3559 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3576 Processing helix chain 'A' and resid 3577 through 3579 No H-bonds generated for 'chain 'A' and resid 3577 through 3579' 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 3615 removed outlier: 3.523A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) Processing helix chain 'A' and resid 3626 through 3636 Processing helix chain 'A' and resid 3639 through 3644 Processing helix chain 'A' and resid 3649 through 3653 removed outlier: 3.909A pdb=" N LEU A3652 " --> pdb=" O SER A3649 " (cutoff:3.500A) Processing helix chain 'A' and resid 3657 through 3671 Processing helix chain 'A' and resid 3686 through 3690 Processing helix chain 'A' and resid 3758 through 3776 removed outlier: 3.825A pdb=" N GLU A3765 " --> pdb=" O ASP A3761 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3784 removed outlier: 4.169A pdb=" N ARG A3784 " --> pdb=" O ALA A3780 " (cutoff:3.500A) Processing helix chain 'A' and resid 3812 through 3820 removed outlier: 3.705A pdb=" N THR A3819 " --> pdb=" O LEU A3815 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A3820 " --> pdb=" O LEU A3816 " (cutoff:3.500A) Processing helix chain 'A' and resid 3821 through 3830 Processing helix chain 'A' and resid 3834 through 3846 Processing helix chain 'A' and resid 3853 through 3862 removed outlier: 3.538A pdb=" N LEU A3857 " --> pdb=" O GLY A3853 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3878 removed outlier: 3.650A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A3878 " --> pdb=" O ARG A3874 " (cutoff:3.500A) Processing helix chain 'A' and resid 3881 through 3891 Processing helix chain 'A' and resid 3893 through 3919 removed outlier: 3.886A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (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 3970 through 3972 No H-bonds generated for 'chain 'A' and resid 3970 through 3972' Processing helix chain 'A' and resid 3978 through 3994 removed outlier: 3.511A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP A3994 " --> pdb=" O ALA A3990 " (cutoff:3.500A) Processing helix chain 'A' and resid 3995 through 4007 Processing helix chain 'A' and resid 4012 through 4022 Processing helix chain 'A' and resid 4039 through 4052 removed outlier: 4.195A pdb=" N TYR A4046 " --> pdb=" O GLN A4042 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A4047 " --> pdb=" O LYS A4043 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A4051 " --> pdb=" O ALA A4047 " (cutoff:3.500A) Processing helix chain 'A' and resid 4055 through 4068 Processing helix chain 'A' and resid 4073 through 4083 Processing helix chain 'A' and resid 4099 through 4112 removed outlier: 3.881A pdb=" N LYS A4105 " --> pdb=" O GLU A4101 " (cutoff:3.500A) Processing helix chain 'A' and resid 4113 through 4118 Processing helix chain 'A' and resid 4119 through 4120 No H-bonds generated for 'chain 'A' and resid 4119 through 4120' Processing helix chain 'A' and resid 4121 through 4125 Processing helix chain 'A' and resid 5009 through 5014 removed outlier: 4.203A pdb=" N UNK A5012 " --> pdb=" O UNK A5009 " (cutoff:3.500A) Processing helix chain 'A' and resid 6002 through 6016 removed outlier: 3.673A pdb=" N UNK A6007 " --> pdb=" O UNK A6003 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N UNK A6011 " --> pdb=" O UNK A6007 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N UNK A6012 " --> pdb=" O UNK A6008 " (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 1537 through 1540 removed outlier: 3.605A pdb=" N PHE A1553 " --> pdb=" O LEU A1538 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A1551 " --> pdb=" O THR A1540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2587 through 2588 Processing sheet with id=AA5, first strand: chain 'A' and resid 3719 through 3722 removed outlier: 3.890A pdb=" N LYS A3736 " --> pdb=" O VAL A3752 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A3738 " --> pdb=" O PHE A3750 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A3801 " --> pdb=" O LYS A3753 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A3800 " --> pdb=" O MET A3796 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A3796 " --> pdb=" O LEU A3800 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3809 through 3811 1544 hydrogen bonds defined for protein. 4521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.34 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9479 1.34 - 1.46: 6044 1.46 - 1.58: 14124 1.58 - 1.70: 0 1.70 - 1.81: 302 Bond restraints: 29949 Sorted by residual: bond pdb=" C GLN A 399 " pdb=" N THR A 400 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.50e+00 bond pdb=" CG1 ILE A1341 " pdb=" CD1 ILE A1341 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.55e+00 bond pdb=" C ASP A1019 " pdb=" N PRO A1020 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 2.99e+00 bond pdb=" CA LYS A2441 " pdb=" C LYS A2441 " ideal model delta sigma weight residual 1.522 1.493 0.029 1.72e-02 3.38e+03 2.84e+00 bond pdb=" N PHE A 446 " pdb=" CA PHE A 446 " ideal model delta sigma weight residual 1.463 1.453 0.010 6.90e-03 2.10e+04 1.99e+00 ... (remaining 29944 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.15: 481 104.15 - 111.62: 13893 111.62 - 119.08: 10681 119.08 - 126.55: 15043 126.55 - 134.02: 399 Bond angle restraints: 40497 Sorted by residual: angle pdb=" N THR A3547 " pdb=" CA THR A3547 " pdb=" C THR A3547 " ideal model delta sigma weight residual 114.56 107.31 7.25 1.27e+00 6.20e-01 3.26e+01 angle pdb=" CB MET A1927 " pdb=" CG MET A1927 " pdb=" SD MET A1927 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N ILE A3471 " pdb=" CA ILE A3471 " pdb=" C ILE A3471 " ideal model delta sigma weight residual 113.39 108.71 4.68 1.47e+00 4.63e-01 1.01e+01 angle pdb=" N SER A3684 " pdb=" CA SER A3684 " pdb=" C SER A3684 " ideal model delta sigma weight residual 109.81 116.80 -6.99 2.21e+00 2.05e-01 1.00e+01 angle pdb=" CA THR A3547 " pdb=" C THR A3547 " pdb=" N GLY A3548 " ideal model delta sigma weight residual 119.26 115.73 3.53 1.14e+00 7.69e-01 9.60e+00 ... (remaining 40492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16383 17.95 - 35.91: 1574 35.91 - 53.86: 243 53.86 - 71.81: 58 71.81 - 89.77: 24 Dihedral angle restraints: 18282 sinusoidal: 7402 harmonic: 10880 Sorted by residual: dihedral pdb=" CA PRO A3685 " pdb=" C PRO A3685 " pdb=" N TRP A3686 " pdb=" CA TRP A3686 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER A3366 " pdb=" C SER A3366 " pdb=" N SER A3367 " pdb=" CA SER A3367 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA MET A3974 " pdb=" C MET A3974 " pdb=" N LYS A3975 " pdb=" CA LYS A3975 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 18279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2937 0.037 - 0.074: 1267 0.074 - 0.110: 352 0.110 - 0.147: 49 0.147 - 0.184: 6 Chirality restraints: 4611 Sorted by residual: chirality pdb=" CB ILE A2476 " pdb=" CA ILE A2476 " pdb=" CG1 ILE A2476 " pdb=" CG2 ILE A2476 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA MET A2443 " pdb=" N MET A2443 " pdb=" C MET A2443 " pdb=" CB MET A2443 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ASP A1019 " pdb=" N ASP A1019 " pdb=" C ASP A1019 " pdb=" CB ASP A1019 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 4608 not shown) Planarity restraints: 5145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A3684 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A3685 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A3685 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A3685 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1019 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A1020 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A1020 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1020 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A3676 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A3677 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A3677 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A3677 " 0.030 5.00e-02 4.00e+02 ... (remaining 5142 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3315 2.74 - 3.28: 33289 3.28 - 3.82: 48939 3.82 - 4.36: 57010 4.36 - 4.90: 93246 Nonbonded interactions: 235799 Sorted by model distance: nonbonded pdb=" O THR A2192 " pdb=" OG SER A2195 " model vdw 2.199 2.440 nonbonded pdb=" O LEU A 57 " pdb=" OG SER A 60 " model vdw 2.204 2.440 nonbonded pdb=" O VAL A1889 " pdb=" ND2 ASN A1909 " model vdw 2.210 2.520 nonbonded pdb=" OG SER A 537 " pdb=" OD1 ASN A 561 " model vdw 2.210 2.440 nonbonded pdb=" ND2 ASN A2365 " pdb=" OE2 GLU A2399 " model vdw 2.211 2.520 ... (remaining 235794 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.820 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: 0.000 Extract box with map and model: 16.700 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 85.940 Find NCS groups from input model: 0.970 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.005 0.074 29949 Z= 0.309 Angle : 0.693 9.637 40497 Z= 0.380 Chirality : 0.042 0.184 4611 Planarity : 0.004 0.112 5145 Dihedral : 14.484 89.768 11188 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % 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: -0.76 (0.14), residues: 3632 helix: 0.27 (0.11), residues: 2266 sheet: -1.37 (0.60), residues: 61 loop : -1.78 (0.18), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 3.413 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.4382 time to fit residues: 123.4319 Evaluate side-chains 138 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.791 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 188 optimal weight: 50.0000 chunk 149 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 175 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 HIS A1426 GLN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2777 HIS A2954 GLN A3112 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29949 Z= 0.229 Angle : 0.616 11.437 40497 Z= 0.316 Chirality : 0.041 0.168 4611 Planarity : 0.004 0.103 5145 Dihedral : 5.004 29.488 3960 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.43 % Allowed : 7.22 % Favored : 92.35 % 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: -0.22 (0.15), residues: 3632 helix: 0.78 (0.11), residues: 2305 sheet: -0.94 (0.63), residues: 61 loop : -1.83 (0.18), residues: 1266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 165 average time/residue: 0.4582 time to fit residues: 128.5929 Evaluate side-chains 153 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 3.808 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3347 time to fit residues: 7.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 278 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1426 GLN ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29949 Z= 0.167 Angle : 0.564 9.630 40497 Z= 0.287 Chirality : 0.039 0.160 4611 Planarity : 0.004 0.094 5145 Dihedral : 4.731 30.096 3960 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.74 % Allowed : 10.34 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3632 helix: 1.01 (0.11), residues: 2306 sheet: -0.80 (0.64), residues: 63 loop : -1.76 (0.18), residues: 1263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.4184 time to fit residues: 132.3468 Evaluate side-chains 159 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 3.488 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3048 time to fit residues: 11.0232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 336 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 319 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 29949 Z= 0.296 Angle : 0.613 8.465 40497 Z= 0.310 Chirality : 0.040 0.156 4611 Planarity : 0.004 0.101 5145 Dihedral : 4.747 28.131 3960 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.84 % Allowed : 12.51 % Favored : 86.65 % 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: 3632 helix: 1.04 (0.11), residues: 2302 sheet: -0.71 (0.64), residues: 61 loop : -1.78 (0.18), residues: 1269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 171 average time/residue: 0.4079 time to fit residues: 120.2538 Evaluate side-chains 156 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3402 time to fit residues: 11.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 3.9990 chunk 202 optimal weight: 0.3980 chunk 5 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2543 ASN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29949 Z= 0.189 Angle : 0.567 8.960 40497 Z= 0.287 Chirality : 0.039 0.173 4611 Planarity : 0.004 0.094 5145 Dihedral : 4.632 29.221 3960 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.62 % Allowed : 14.06 % Favored : 85.32 % 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: 3632 helix: 1.16 (0.11), residues: 2293 sheet: -0.52 (0.65), residues: 61 loop : -1.73 (0.19), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 166 average time/residue: 0.4026 time to fit residues: 114.4772 Evaluate side-chains 155 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 3.220 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2732 time to fit residues: 8.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 0.0060 chunk 321 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 29949 Z= 0.158 Angle : 0.549 10.596 40497 Z= 0.277 Chirality : 0.039 0.167 4611 Planarity : 0.004 0.091 5145 Dihedral : 4.477 28.361 3960 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.65 % Allowed : 14.87 % Favored : 84.48 % 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: 0.34 (0.15), residues: 3632 helix: 1.28 (0.11), residues: 2280 sheet: -0.28 (0.65), residues: 61 loop : -1.71 (0.19), residues: 1291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 175 average time/residue: 0.3900 time to fit residues: 116.9619 Evaluate side-chains 157 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2823 time to fit residues: 9.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 355 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29949 Z= 0.185 Angle : 0.577 12.205 40497 Z= 0.287 Chirality : 0.039 0.159 4611 Planarity : 0.004 0.090 5145 Dihedral : 4.449 28.168 3960 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.43 % Allowed : 15.70 % Favored : 83.86 % 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: 0.38 (0.15), residues: 3632 helix: 1.33 (0.11), residues: 2274 sheet: -0.28 (0.65), residues: 61 loop : -1.71 (0.18), residues: 1297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 161 average time/residue: 0.4053 time to fit residues: 112.2420 Evaluate side-chains 153 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3067 time to fit residues: 8.0146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 212 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 409 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29949 Z= 0.157 Angle : 0.568 13.010 40497 Z= 0.282 Chirality : 0.039 0.282 4611 Planarity : 0.004 0.088 5145 Dihedral : 4.378 27.036 3960 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.40 % Allowed : 16.29 % Favored : 83.31 % 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: 0.44 (0.15), residues: 3632 helix: 1.39 (0.11), residues: 2271 sheet: -0.22 (0.66), residues: 61 loop : -1.70 (0.18), residues: 1300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 3.441 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 172 average time/residue: 0.4151 time to fit residues: 122.2466 Evaluate side-chains 147 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 3.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2902 time to fit residues: 5.5685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 10.0000 chunk 340 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29949 Z= 0.186 Angle : 0.601 13.294 40497 Z= 0.293 Chirality : 0.039 0.316 4611 Planarity : 0.004 0.089 5145 Dihedral : 4.358 25.486 3960 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.06 % Allowed : 17.10 % Favored : 82.84 % 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: 0.46 (0.15), residues: 3632 helix: 1.39 (0.11), residues: 2283 sheet: -0.20 (0.66), residues: 61 loop : -1.70 (0.18), residues: 1288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 3.733 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 148 average time/residue: 0.4210 time to fit residues: 108.4331 Evaluate side-chains 146 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2870 time to fit residues: 5.3387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 367 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 chunk 292 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29949 Z= 0.276 Angle : 0.638 13.586 40497 Z= 0.312 Chirality : 0.040 0.224 4611 Planarity : 0.004 0.092 5145 Dihedral : 4.462 25.693 3960 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.12 % Allowed : 17.16 % Favored : 82.72 % 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: 0.44 (0.15), residues: 3632 helix: 1.36 (0.11), residues: 2290 sheet: -0.34 (0.66), residues: 61 loop : -1.68 (0.19), residues: 1281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 3.405 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 153 average time/residue: 0.4147 time to fit residues: 108.7440 Evaluate side-chains 151 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 3.663 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2800 time to fit residues: 6.4143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 301 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2859 GLN ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.060370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045273 restraints weight = 158047.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.047033 restraints weight = 80686.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048218 restraints weight = 52464.063| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29949 Z= 0.166 Angle : 0.602 13.243 40497 Z= 0.294 Chirality : 0.039 0.195 4611 Planarity : 0.004 0.088 5145 Dihedral : 4.397 26.551 3960 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.22 % Allowed : 17.37 % Favored : 82.41 % 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: 0.48 (0.15), residues: 3632 helix: 1.38 (0.11), residues: 2293 sheet: -0.26 (0.66), residues: 61 loop : -1.66 (0.19), residues: 1278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.10 seconds wall clock time: 88 minutes 53.13 seconds (5333.13 seconds total)