Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 01:09:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z88_14546/05_2023/7z88_14546_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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: 7 Type Number sf(0) Gaussians P 52 5.49 5 S 227 5.16 5 Cl 1 4.86 5 C 24682 2.51 5 N 6575 2.21 5 O 7216 1.98 5 F 1 1.80 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 GLU 80": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 854": "NH1" <-> "NH2" Residue "A GLU 889": "OE1" <-> "OE2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ASP 1019": "OD1" <-> "OD2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A ASP 1588": "OD1" <-> "OD2" Residue "A ARG 1608": "NH1" <-> "NH2" Residue "A PHE 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A ARG 1727": "NH1" <-> "NH2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1787": "NH1" <-> "NH2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A GLU 1910": "OE1" <-> "OE2" Residue "A TYR 1920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A TYR 1962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A TYR 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2228": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A PHE 2257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A PHE 2384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2406": "OE1" <-> "OE2" Residue "A TYR 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A ASP 2482": "OD1" <-> "OD2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A PHE 2809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2940": "NH1" <-> "NH2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A GLU 2995": "OE1" <-> "OE2" Residue "A TYR 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3012": "OE1" <-> "OE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A PHE 3144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3159": "NH1" <-> "NH2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3247": "NH1" <-> "NH2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3361": "OE1" <-> "OE2" Residue "A PHE 3382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3411": "OD1" <-> "OD2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A TYR 3531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3570": "OD1" <-> "OD2" Residue "A ARG 3593": "NH1" <-> "NH2" Residue "A GLU 3611": "OE1" <-> "OE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3700": "OE1" <-> "OE2" Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3718": "NH1" <-> "NH2" Residue "A ARG 3746": "NH1" <-> "NH2" Residue "A ARG 3759": "NH1" <-> "NH2" Residue "A ARG 3763": "NH1" <-> "NH2" Residue "A ARG 3833": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3957": "OE1" <-> "OE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A TYR 3981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4003": "OD1" <-> "OD2" Residue "A ASP 4113": "OD1" <-> "OD2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 288": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C GLU 645": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38754 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 28443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3599, 28443 Classifications: {'peptide': 3599} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PCIS': 1, 'PTRANS': 153, 'TRANS': 3444} Chain breaks: 21 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 33, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 258 Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3937 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5274 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 27, 'TRANS': 633} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "E" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 540 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'1IX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.84, per 1000 atoms: 0.54 Number of scatterers: 38754 At special positions: 0 Unit cell: (131.704, 179.952, 225.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 227 16.00 P 52 15.00 F 1 9.00 O 7216 8.00 N 6575 7.00 C 24682 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: 19.14 Conformation dependent library (CDL) restraints added in 6.1 seconds 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 11 sheets defined 53.6% alpha, 2.9% beta 14 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 22.58 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.799A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.919A pdb=" N GLU A 94 " --> pdb=" O CYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.346A pdb=" N VAL A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.858A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 removed outlier: 4.829A pdb=" N LEU A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 267 through 281 removed outlier: 6.234A pdb=" N SER A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 removed outlier: 3.815A pdb=" N LEU A 287 " --> pdb=" O THR A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 290 through 302 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.891A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 359 through 374 removed outlier: 4.160A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.711A pdb=" N MET A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.914A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 removed outlier: 4.479A pdb=" N CYS A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 535 removed outlier: 3.583A pdb=" N LEU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 646 through 659 Processing helix chain 'A' and resid 666 through 679 Processing helix chain 'A' and resid 701 through 720 removed outlier: 4.352A pdb=" N LYS A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 removed outlier: 3.545A pdb=" N SER A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 750 through 757 removed outlier: 3.593A pdb=" N ALA A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 829 through 836 Processing helix chain 'A' and resid 848 through 861 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 908 through 919 Proline residue: A 912 - end of helix removed outlier: 3.667A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 944 Processing helix chain 'A' and resid 959 through 973 removed outlier: 3.714A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 4.039A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 995 removed outlier: 4.495A pdb=" N TYR A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) Proline residue: A 986 - end of helix Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1023 through 1043 removed outlier: 3.734A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1075 through 1085 Processing helix chain 'A' and resid 1102 through 1115 removed outlier: 3.994A pdb=" N VAL A1105 " --> pdb=" O GLU A1102 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A1106 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A1114 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1123 through 1144 removed outlier: 3.925A pdb=" N ILE A1137 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1174 Processing helix chain 'A' and resid 1181 through 1197 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1204 through 1214 removed outlier: 4.033A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.680A pdb=" N LEU A1220 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1221 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A1223 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1271 Processing helix chain 'A' and resid 1278 through 1281 No H-bonds generated for 'chain 'A' and resid 1278 through 1281' Processing helix chain 'A' and resid 1284 through 1286 No H-bonds generated for 'chain 'A' and resid 1284 through 1286' Processing helix chain 'A' and resid 1290 through 1299 Processing helix chain 'A' and resid 1326 through 1349 removed outlier: 3.993A pdb=" N VAL A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'A' and resid 1368 through 1376 Processing helix chain 'A' and resid 1379 through 1382 removed outlier: 3.508A pdb=" N ILE A1382 " --> pdb=" O PRO A1379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1379 through 1382' Processing helix chain 'A' and resid 1390 through 1408 Proline residue: A1396 - end of helix removed outlier: 3.740A pdb=" N VAL A1400 " --> pdb=" O PRO A1396 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET A1408 " --> pdb=" O LYS A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1422 removed outlier: 4.186A pdb=" N GLU A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A1422 " --> pdb=" O HIS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1441 through 1460 Processing helix chain 'A' and resid 1478 through 1490 Processing helix chain 'A' and resid 1506 through 1521 Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1557 through 1563 removed outlier: 3.747A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1573 removed outlier: 3.529A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1585 removed outlier: 4.270A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1606 Processing helix chain 'A' and resid 1614 through 1624 Processing helix chain 'A' and resid 1641 through 1655 Processing helix chain 'A' and resid 1668 through 1678 removed outlier: 3.877A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1692 Processing helix chain 'A' and resid 1696 through 1698 No H-bonds generated for 'chain 'A' and resid 1696 through 1698' Processing helix chain 'A' and resid 1704 through 1721 Processing helix chain 'A' and resid 1736 through 1752 Processing helix chain 'A' and resid 1756 through 1766 Processing helix chain 'A' and resid 1775 through 1786 Processing helix chain 'A' and resid 1791 through 1806 Processing helix chain 'A' and resid 1813 through 1821 removed outlier: 3.742A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1838 through 1851 removed outlier: 5.121A pdb=" N VAL A1845 " --> pdb=" O SER A1841 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP A1846 " --> pdb=" O THR A1842 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1883 Processing helix chain 'A' and resid 1887 through 1890 No H-bonds generated for 'chain 'A' and resid 1887 through 1890' Processing helix chain 'A' and resid 1910 through 1920 Processing helix chain 'A' and resid 1934 through 1952 Processing helix chain 'A' and resid 1961 through 1964 No H-bonds generated for 'chain 'A' and resid 1961 through 1964' Processing helix chain 'A' and resid 1977 through 1981 Processing helix chain 'A' and resid 2038 through 2045 removed outlier: 3.677A pdb=" N PHE A2043 " --> pdb=" O GLU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2105 Processing helix chain 'A' and resid 2126 through 2134 Processing helix chain 'A' and resid 2140 through 2152 Processing helix chain 'A' and resid 2154 through 2158 removed outlier: 3.673A pdb=" N ARG A2158 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2173 Processing helix chain 'A' and resid 2183 through 2195 Processing helix chain 'A' and resid 2206 through 2221 Processing helix chain 'A' and resid 2228 through 2244 Processing helix chain 'A' and resid 2256 through 2260 Processing helix chain 'A' and resid 2271 through 2282 Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 3.913A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2332 Processing helix chain 'A' and resid 2338 through 2353 removed outlier: 3.794A pdb=" N LEU A2344 " --> pdb=" O SER A2340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A2352 " --> pdb=" O GLN A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2370 removed outlier: 4.524A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2388 Proline residue: A2387 - end of helix Processing helix chain 'A' and resid 2392 through 2404 removed outlier: 3.890A 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 2420 through 2423 No H-bonds generated for 'chain 'A' and resid 2420 through 2423' Processing helix chain 'A' and resid 2429 through 2441 Processing helix chain 'A' and resid 2443 through 2445 No H-bonds generated for 'chain 'A' and resid 2443 through 2445' Processing helix chain 'A' and resid 2448 through 2461 removed outlier: 3.646A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A2456 " --> pdb=" O ARG A2452 " (cutoff:3.500A) Proline residue: A2457 - end of helix removed outlier: 4.515A pdb=" N PHE A2461 " --> pdb=" O PRO A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2467 through 2482 removed outlier: 3.948A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2507 removed outlier: 4.897A pdb=" N PHE A2499 " --> pdb=" O SER A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2517 through 2526 Processing helix chain 'A' and resid 2537 through 2545 removed outlier: 3.845A pdb=" N ASN A2543 " --> pdb=" O LEU A2539 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A2544 " --> pdb=" O LEU A2540 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A2545 " --> pdb=" O ALA A2541 " (cutoff:3.500A) Processing helix chain 'A' and resid 2554 through 2564 Processing helix chain 'A' and resid 2791 through 2799 removed outlier: 3.525A pdb=" N GLN A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2802 through 2819 Processing helix chain 'A' and resid 2826 through 2846 Processing helix chain 'A' and resid 2852 through 2861 Processing helix chain 'A' and resid 2867 through 2869 No H-bonds generated for 'chain 'A' and resid 2867 through 2869' Processing helix chain 'A' and resid 2873 through 2883 Processing helix chain 'A' and resid 2886 through 2896 Processing helix chain 'A' and resid 2918 through 2932 removed outlier: 4.636A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A2932 " --> pdb=" O LYS A2928 " (cutoff:3.500A) Processing helix chain 'A' and resid 2936 through 2940 Processing helix chain 'A' and resid 2952 through 2961 Processing helix chain 'A' and resid 2967 through 2976 Processing helix chain 'A' and resid 2988 through 3004 removed outlier: 3.828A pdb=" N PHE A2993 " --> pdb=" O ALA A2989 " (cutoff:3.500A) Processing helix chain 'A' and resid 3008 through 3017 Processing helix chain 'A' and resid 3035 through 3055 Proline residue: A3042 - end of helix removed outlier: 3.638A pdb=" N GLY A3055 " --> pdb=" O LEU A3051 " (cutoff:3.500A) Processing helix chain 'A' and resid 3061 through 3068 Processing helix chain 'A' and resid 3073 through 3081 removed outlier: 4.146A pdb=" N ILE A3077 " --> pdb=" O LEU A3073 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A3078 " --> pdb=" O GLN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3085 through 3093 Processing helix chain 'A' and resid 3096 through 3114 Processing helix chain 'A' and resid 3124 through 3146 removed outlier: 3.986A pdb=" N SER A3131 " --> pdb=" O THR A3127 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A3132 " --> pdb=" O LYS A3128 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A3134 " --> pdb=" O GLN A3130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A3146 " --> pdb=" O ILE A3142 " (cutoff:3.500A) Processing helix chain 'A' and resid 3149 through 3151 No H-bonds generated for 'chain 'A' and resid 3149 through 3151' Processing helix chain 'A' and resid 3155 through 3166 Processing helix chain 'A' and resid 3176 through 3196 Processing helix chain 'A' and resid 3228 through 3249 Processing helix chain 'A' and resid 3252 through 3263 Processing helix chain 'A' and resid 3270 through 3288 Processing helix chain 'A' and resid 3293 through 3301 Processing helix chain 'A' and resid 3305 through 3308 No H-bonds generated for 'chain 'A' and resid 3305 through 3308' Processing helix chain 'A' and resid 3320 through 3341 Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3373 through 3390 Processing helix chain 'A' and resid 3408 through 3427 Processing helix chain 'A' and resid 3442 through 3455 removed outlier: 4.797A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3460 through 3462 No H-bonds generated for 'chain 'A' and resid 3460 through 3462' Processing helix chain 'A' and resid 3465 through 3474 Processing helix chain 'A' and resid 3481 through 3488 Processing helix chain 'A' and resid 3496 through 3507 removed outlier: 5.720A pdb=" N SER A3500 " --> pdb=" O SER A3497 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A3503 " --> pdb=" O SER A3500 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A3506 " --> pdb=" O VAL A3503 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3514 Processing helix chain 'A' and resid 3516 through 3524 removed outlier: 3.825A pdb=" N ASP A3523 " --> pdb=" O GLU A3519 " (cutoff:3.500A) Processing helix chain 'A' and resid 3536 through 3539 No H-bonds generated for 'chain 'A' and resid 3536 through 3539' Processing helix chain 'A' and resid 3548 through 3562 Processing helix chain 'A' and resid 3568 through 3578 Processing helix chain 'A' and resid 3581 through 3595 Processing helix chain 'A' and resid 3605 through 3614 removed outlier: 4.382A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3626 removed outlier: 4.050A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3631 through 3636 Processing helix chain 'A' and resid 3642 through 3649 removed outlier: 3.634A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3661 through 3673 Processing helix chain 'A' and resid 3681 through 3683 No H-bonds generated for 'chain 'A' and resid 3681 through 3683' Processing helix chain 'A' and resid 3685 through 3688 No H-bonds generated for 'chain 'A' and resid 3685 through 3688' Processing helix chain 'A' and resid 3759 through 3777 Processing helix chain 'A' and resid 3779 through 3783 Processing helix chain 'A' and resid 3812 through 3819 Processing helix chain 'A' and resid 3822 through 3829 Processing helix chain 'A' and resid 3835 through 3847 Processing helix chain 'A' and resid 3854 through 3860 removed outlier: 4.420A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3877 removed outlier: 3.908A pdb=" N LYS A3877 " --> pdb=" O LYS A3873 " (cutoff:3.500A) Processing helix chain 'A' and resid 3883 through 3889 Processing helix chain 'A' and resid 3894 through 3917 Processing helix chain 'A' and resid 3925 through 3927 No H-bonds generated for 'chain 'A' and resid 3925 through 3927' Processing helix chain 'A' and resid 3965 through 3971 removed outlier: 4.167A pdb=" N MET A3971 " --> pdb=" O PHE A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3982 through 3991 Processing helix chain 'A' and resid 3997 through 4006 Processing helix chain 'A' and resid 4040 through 4049 Processing helix chain 'A' and resid 4056 through 4067 Processing helix chain 'A' and resid 4074 through 4082 Processing helix chain 'A' and resid 4100 through 4111 Processing helix chain 'A' and resid 4114 through 4117 No H-bonds generated for 'chain 'A' and resid 4114 through 4117' Processing helix chain 'A' and resid 4122 through 4124 No H-bonds generated for 'chain 'A' and resid 4122 through 4124' Processing helix chain 'B' and resid 59 through 77 removed outlier: 3.855A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.844A pdb=" N GLN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 378 through 391 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 522 through 529 removed outlier: 4.151A pdb=" N VAL B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 108 through 121 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 372 through 386 removed outlier: 4.328A pdb=" N ASP C 386 " --> pdb=" O HIS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 460 Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 520 through 536 removed outlier: 5.276A pdb=" N ILE C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Proline residue: C 529 - end of helix Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 611 through 625 Processing helix chain 'C' and resid 629 through 648 Processing helix chain 'C' and resid 653 through 668 Processing helix chain 'C' and resid 672 through 681 removed outlier: 3.873A pdb=" N ASP C 681 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 704 Processing sheet with id= A, first strand: chain 'A' and resid 893 through 896 Processing sheet with id= B, first strand: chain 'A' and resid 3736 through 3738 removed outlier: 6.438A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id= D, first strand: chain 'B' and resid 198 through 201 removed outlier: 6.815A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 82 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE B 40 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 84 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 42 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 86 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 258 through 262 Processing sheet with id= F, first strand: chain 'B' and resid 318 through 322 Processing sheet with id= G, first strand: chain 'B' and resid 350 through 352 Processing sheet with id= H, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.246A pdb=" N LYS C 129 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 11 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS C 131 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N CYS C 13 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU C 133 " --> pdb=" O CYS C 13 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP C 15 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE C 135 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN C 162 " --> pdb=" O ILE C 134 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 246 through 253 removed outlier: 4.566A pdb=" N ALA C 366 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N SER C 266 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU C 362 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 364 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 392 through 395 Processing sheet with id= K, first strand: chain 'C' and resid 464 through 466 removed outlier: 4.246A pdb=" N LYS C 465 " --> pdb=" O GLU C 474 " (cutoff:3.500A) 1618 hydrogen bonds defined for protein. 4746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 23.85 Time building geometry restraints manager: 20.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12162 1.34 - 1.46: 8810 1.46 - 1.59: 18203 1.59 - 1.71: 102 1.71 - 1.83: 359 Bond restraints: 39636 Sorted by residual: bond pdb=" C11 1IX A4201 " pdb="CL1 1IX A4201 " ideal model delta sigma weight residual 1.728 1.833 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C24 1IX A4201 " pdb=" N26 1IX A4201 " ideal model delta sigma weight residual 1.371 1.475 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C12 1IX A4201 " pdb=" C13 1IX A4201 " ideal model delta sigma weight residual 1.379 1.471 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C14 1IX A4201 " pdb=" C16 1IX A4201 " ideal model delta sigma weight residual 1.480 1.565 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C ASP A2289 " pdb=" N PRO A2290 " ideal model delta sigma weight residual 1.331 1.365 -0.033 7.90e-03 1.60e+04 1.76e+01 ... (remaining 39631 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.38: 554 103.38 - 111.19: 15645 111.19 - 119.00: 16875 119.00 - 126.81: 20154 126.81 - 134.62: 569 Bond angle restraints: 53797 Sorted by residual: angle pdb=" C SER A2547 " pdb=" N PRO A2548 " pdb=" CA PRO A2548 " ideal model delta sigma weight residual 119.84 134.62 -14.78 1.25e+00 6.40e-01 1.40e+02 angle pdb=" N VAL A 407 " pdb=" CA VAL A 407 " pdb=" C VAL A 407 " ideal model delta sigma weight residual 113.53 107.38 6.15 9.80e-01 1.04e+00 3.94e+01 angle pdb=" N ARG A3965 " pdb=" CA ARG A3965 " pdb=" C ARG A3965 " ideal model delta sigma weight residual 111.33 118.64 -7.31 1.21e+00 6.83e-01 3.65e+01 angle pdb=" N VAL A 976 " pdb=" CA VAL A 976 " pdb=" C VAL A 976 " ideal model delta sigma weight residual 110.62 115.78 -5.16 1.02e+00 9.61e-01 2.56e+01 angle pdb=" C LEU A1639 " pdb=" N GLU A1640 " pdb=" CA GLU A1640 " ideal model delta sigma weight residual 122.08 129.68 -7.60 1.53e+00 4.27e-01 2.47e+01 ... (remaining 53792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 22666 28.04 - 56.08: 1212 56.08 - 84.12: 122 84.12 - 112.17: 10 112.17 - 140.21: 2 Dihedral angle restraints: 24012 sinusoidal: 10044 harmonic: 13968 Sorted by residual: dihedral pdb=" CA PRO A1020 " pdb=" C PRO A1020 " pdb=" N VAL A1021 " pdb=" CA VAL A1021 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA ARG A3462 " pdb=" C ARG A3462 " pdb=" N LEU A3463 " pdb=" CA LEU A3463 " ideal model delta harmonic sigma weight residual -180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA ARG B 252 " pdb=" C ARG B 252 " pdb=" N LYS B 253 " pdb=" CA LYS B 253 " ideal model delta harmonic sigma weight residual 180.00 147.20 32.80 0 5.00e+00 4.00e-02 4.30e+01 ... (remaining 24009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 5095 0.063 - 0.127: 918 0.127 - 0.190: 105 0.190 - 0.253: 12 0.253 - 0.317: 5 Chirality restraints: 6135 Sorted by residual: chirality pdb=" CG LEU A3005 " pdb=" CB LEU A3005 " pdb=" CD1 LEU A3005 " pdb=" CD2 LEU A3005 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE A2336 " pdb=" CA ILE A2336 " pdb=" CG1 ILE A2336 " pdb=" CG2 ILE A2336 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA TYR A3531 " pdb=" N TYR A3531 " pdb=" C TYR A3531 " pdb=" CB TYR A3531 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 6132 not shown) Planarity restraints: 6660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A4055 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A4056 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO A4056 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A4056 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 634 " -0.063 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO A 635 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 635 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 635 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A4005 " 0.025 2.00e-02 2.50e+03 2.89e-02 1.47e+01 pdb=" CG PHE A4005 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A4005 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A4005 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A4005 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A4005 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A4005 " 0.003 2.00e-02 2.50e+03 ... (remaining 6657 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1915 2.71 - 3.26: 42274 3.26 - 3.80: 64533 3.80 - 4.35: 83236 4.35 - 4.90: 130967 Nonbonded interactions: 322925 Sorted by model distance: nonbonded pdb=" OE1 GLU A3478 " pdb=" OG1 THR A3479 " model vdw 2.160 2.440 nonbonded pdb=" OD2 ASP B 505 " pdb=" OH TYR C 333 " model vdw 2.195 2.440 nonbonded pdb=" O GLU A1769 " pdb=" NH2 ARG A1822 " model vdw 2.203 2.520 nonbonded pdb=" O CYS A 931 " pdb=" OH TYR A 984 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR A3828 " pdb=" OE1 GLU A4125 " model vdw 2.215 2.440 ... (remaining 322920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.520 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: 0.030 Extract box with map and model: 12.550 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 119.120 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.140 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 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 0.105 39636 Z= 0.336 Angle : 0.917 14.776 53797 Z= 0.500 Chirality : 0.050 0.317 6135 Planarity : 0.006 0.111 6660 Dihedral : 16.250 140.207 14900 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.29 % Favored : 88.62 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.11), residues: 4694 helix: -1.29 (0.09), residues: 2710 sheet: -2.56 (0.32), residues: 212 loop : -3.47 (0.13), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 690 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 697 average time/residue: 0.5604 time to fit residues: 632.6233 Evaluate side-chains 587 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 585 time to evaluate : 4.388 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7430 time to fit residues: 8.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 403 optimal weight: 0.9980 chunk 362 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 193 optimal weight: 0.0770 chunk 374 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 434 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS B 158 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 39636 Z= 0.278 Angle : 0.755 10.769 53797 Z= 0.383 Chirality : 0.045 0.242 6135 Planarity : 0.005 0.076 6660 Dihedral : 12.515 141.442 5606 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.59 % Favored : 88.33 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.12), residues: 4694 helix: -0.73 (0.10), residues: 2733 sheet: -2.30 (0.33), residues: 202 loop : -3.27 (0.13), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 637 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 35 residues processed: 655 average time/residue: 0.5527 time to fit residues: 590.6910 Evaluate side-chains 634 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 599 time to evaluate : 4.435 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3923 time to fit residues: 33.2011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 241 optimal weight: 0.2980 chunk 134 optimal weight: 5.9990 chunk 361 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 434 optimal weight: 1.9990 chunk 469 optimal weight: 9.9990 chunk 387 optimal weight: 0.9990 chunk 431 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 348 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 827 ASN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3743 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 39636 Z= 0.251 Angle : 0.702 10.311 53797 Z= 0.356 Chirality : 0.043 0.231 6135 Planarity : 0.005 0.063 6660 Dihedral : 12.380 142.175 5606 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.78 % Favored : 89.16 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4694 helix: -0.39 (0.10), residues: 2745 sheet: -2.17 (0.33), residues: 197 loop : -3.13 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 629 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 32 residues processed: 677 average time/residue: 0.5498 time to fit residues: 608.0211 Evaluate side-chains 627 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 595 time to evaluate : 4.731 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3805 time to fit residues: 29.7544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 225 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 436 optimal weight: 0.7980 chunk 462 optimal weight: 10.0000 chunk 228 optimal weight: 0.5980 chunk 413 optimal weight: 20.0000 chunk 124 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1772 HIS ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 ASN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 39636 Z= 0.224 Angle : 0.673 13.392 53797 Z= 0.341 Chirality : 0.042 0.227 6135 Planarity : 0.005 0.082 6660 Dihedral : 12.259 143.016 5606 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.65 % Favored : 89.28 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.93 (0.12), residues: 4694 helix: -0.16 (0.10), residues: 2740 sheet: -2.00 (0.34), residues: 197 loop : -3.03 (0.14), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 624 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 38 residues processed: 673 average time/residue: 0.5589 time to fit residues: 615.2273 Evaluate side-chains 640 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 602 time to evaluate : 4.422 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3812 time to fit residues: 34.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 384 optimal weight: 1.9990 chunk 262 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 344 optimal weight: 0.7980 chunk 190 optimal weight: 0.0770 chunk 394 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 235 optimal weight: 0.1980 chunk 414 optimal weight: 30.0000 chunk 116 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 625 ASN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3326 GLN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 39636 Z= 0.186 Angle : 0.645 11.041 53797 Z= 0.326 Chirality : 0.041 0.208 6135 Planarity : 0.004 0.061 6660 Dihedral : 12.112 144.087 5606 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.84 % Favored : 90.09 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.69 (0.12), residues: 4694 helix: 0.03 (0.10), residues: 2743 sheet: -1.80 (0.34), residues: 197 loop : -2.95 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 639 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 28 residues processed: 686 average time/residue: 0.5446 time to fit residues: 612.6642 Evaluate side-chains 629 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 601 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3798 time to fit residues: 26.3851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 155 optimal weight: 0.9990 chunk 416 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 462 optimal weight: 7.9990 chunk 383 optimal weight: 0.6980 chunk 214 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 152 optimal weight: 0.0010 chunk 242 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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** A 625 ASN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2042 GLN ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2353 GLN ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 39636 Z= 0.222 Angle : 0.662 10.607 53797 Z= 0.334 Chirality : 0.042 0.269 6135 Planarity : 0.004 0.061 6660 Dihedral : 12.106 144.252 5606 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.73 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.63 (0.12), residues: 4694 helix: 0.08 (0.10), residues: 2725 sheet: -1.74 (0.34), residues: 197 loop : -2.90 (0.14), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 626 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 51 residues processed: 670 average time/residue: 0.5760 time to fit residues: 632.3215 Evaluate side-chains 655 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 604 time to evaluate : 4.333 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.3899 time to fit residues: 43.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 445 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 337 optimal weight: 2.9990 chunk 261 optimal weight: 0.0970 chunk 389 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 460 optimal weight: 4.9990 chunk 288 optimal weight: 0.0980 chunk 280 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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** A 827 ASN A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2183 HIS ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 39636 Z= 0.211 Angle : 0.665 9.995 53797 Z= 0.335 Chirality : 0.042 0.261 6135 Planarity : 0.005 0.065 6660 Dihedral : 12.062 144.304 5606 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.25 % Favored : 89.69 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.59 (0.12), residues: 4694 helix: 0.10 (0.10), residues: 2731 sheet: -1.71 (0.34), residues: 197 loop : -2.87 (0.14), residues: 1766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 615 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 646 average time/residue: 0.5546 time to fit residues: 587.3239 Evaluate side-chains 614 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 596 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4020 time to fit residues: 20.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 285 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 292 optimal weight: 2.9990 chunk 313 optimal weight: 0.0980 chunk 227 optimal weight: 0.5980 chunk 42 optimal weight: 0.0000 chunk 362 optimal weight: 2.9990 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3177 ASN A3185 ASN ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 39636 Z= 0.179 Angle : 0.651 12.226 53797 Z= 0.326 Chirality : 0.041 0.258 6135 Planarity : 0.004 0.064 6660 Dihedral : 11.929 144.583 5606 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.24 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.46 (0.12), residues: 4694 helix: 0.21 (0.10), residues: 2747 sheet: -1.49 (0.35), residues: 186 loop : -2.85 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 617 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 642 average time/residue: 0.5676 time to fit residues: 599.7688 Evaluate side-chains 618 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 598 time to evaluate : 4.331 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4122 time to fit residues: 21.5008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 419 optimal weight: 4.9990 chunk 441 optimal weight: 0.1980 chunk 402 optimal weight: 0.3980 chunk 429 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 337 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 387 optimal weight: 0.6980 chunk 406 optimal weight: 5.9990 chunk 427 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** A 477 ASN A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1754 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 ASN ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 39636 Z= 0.214 Angle : 0.676 11.725 53797 Z= 0.338 Chirality : 0.042 0.259 6135 Planarity : 0.004 0.068 6660 Dihedral : 11.930 144.314 5606 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.94 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.12), residues: 4694 helix: 0.18 (0.10), residues: 2748 sheet: -1.59 (0.35), residues: 192 loop : -2.79 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 603 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 616 average time/residue: 0.5603 time to fit residues: 565.6576 Evaluate side-chains 615 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 597 time to evaluate : 5.616 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4041 time to fit residues: 20.2784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 281 optimal weight: 2.9990 chunk 453 optimal weight: 6.9990 chunk 277 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 476 optimal weight: 1.9990 chunk 438 optimal weight: 0.9990 chunk 379 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 292 optimal weight: 1.9990 chunk 232 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3643 HIS ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 39636 Z= 0.226 Angle : 0.682 12.509 53797 Z= 0.341 Chirality : 0.043 0.264 6135 Planarity : 0.004 0.065 6660 Dihedral : 11.932 144.241 5606 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.82 % Favored : 90.12 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.12), residues: 4694 helix: 0.18 (0.10), residues: 2743 sheet: -1.60 (0.35), residues: 192 loop : -2.76 (0.14), residues: 1759 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9388 Ramachandran restraints generated. 4694 Oldfield, 0 Emsley, 4694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 590 time to evaluate : 5.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 592 average time/residue: 0.5959 time to fit residues: 578.8980 Evaluate side-chains 594 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 585 time to evaluate : 4.187 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3885 time to fit residues: 12.6276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 301 optimal weight: 0.2980 chunk 403 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 349 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 390 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN ** A1083 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS B 416 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.238041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.204343 restraints weight = 42777.240| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.04 r_work: 0.3922 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 39636 Z= 0.183 Angle : 0.657 12.685 53797 Z= 0.328 Chirality : 0.041 0.269 6135 Planarity : 0.004 0.063 6660 Dihedral : 11.813 144.378 5606 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.59 % Favored : 90.35 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.30 (0.12), residues: 4694 helix: 0.32 (0.10), residues: 2739 sheet: -1.37 (0.36), residues: 187 loop : -2.76 (0.14), residues: 1768 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: