Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 08:42:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0y_22618/05_2023/7k0y_22618.pdb" } resolution = 3.7 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= 0.003 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: 5 Type Number sf(0) Gaussians P 71 5.49 5 S 233 5.16 5 C 25304 2.51 5 N 6762 2.21 5 O 7465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ARG 1152": "NH1" <-> "NH2" Residue "A ARG 1184": "NH1" <-> "NH2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A ARG 1420": "NH1" <-> "NH2" Residue "A GLU 1421": "OE1" <-> "OE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A GLU 1581": "OE1" <-> "OE2" Residue "A GLU 1640": "OE1" <-> "OE2" Residue "A ARG 1711": "NH1" <-> "NH2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A GLU 1776": "OE1" <-> "OE2" Residue "A ARG 1816": "NH1" <-> "NH2" Residue "A ARG 1822": "NH1" <-> "NH2" Residue "A ARG 1883": "NH1" <-> "NH2" Residue "A ARG 1938": "NH1" <-> "NH2" Residue "A ARG 2143": "NH1" <-> "NH2" Residue "A ARG 2158": "NH1" <-> "NH2" Residue "A ARG 2214": "NH1" <-> "NH2" Residue "A ARG 2232": "NH1" <-> "NH2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "A ARG 2311": "NH1" <-> "NH2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A ARG 2427": "NH1" <-> "NH2" Residue "A ARG 2431": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A ARG 2485": "NH1" <-> "NH2" Residue "A GLU 2490": "OE1" <-> "OE2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2800": "NH1" <-> "NH2" Residue "A ARG 2899": "NH1" <-> "NH2" Residue "A ARG 2962": "NH1" <-> "NH2" Residue "A GLU 2990": "OE1" <-> "OE2" Residue "A ARG 3125": "NH1" <-> "NH2" Residue "A ARG 3232": "NH1" <-> "NH2" Residue "A ARG 3287": "NH1" <-> "NH2" Residue "A ARG 3289": "NH1" <-> "NH2" Residue "A GLU 3309": "OE1" <-> "OE2" Residue "A ARG 3324": "NH1" <-> "NH2" Residue "A ARG 3335": "NH1" <-> "NH2" Residue "A GLU 3344": "OE1" <-> "OE2" Residue "A GLU 3429": "OE1" <-> "OE2" Residue "A ARG 3462": "NH1" <-> "NH2" Residue "A ARG 3467": "NH1" <-> "NH2" Residue "A ARG 3474": "NH1" <-> "NH2" Residue "A GLU 3520": "OE1" <-> "OE2" Residue "A GLU 3553": "OE1" <-> "OE2" Residue "A GLU 3611": "OE1" <-> "OE2" Residue "A ARG 3629": "NH1" <-> "NH2" Residue "A ARG 3630": "NH1" <-> "NH2" Residue "A ARG 3653": "NH1" <-> "NH2" Residue "A ARG 3696": "NH1" <-> "NH2" Residue "A GLU 3698": "OE1" <-> "OE2" Residue "A ARG 3708": "NH1" <-> "NH2" Residue "A GLU 3714": "OE1" <-> "OE2" Residue "A ARG 3718": "NH1" <-> "NH2" Residue "A ARG 3733": "NH1" <-> "NH2" Residue "A ARG 3734": "NH1" <-> "NH2" Residue "A GLU 3756": "OE1" <-> "OE2" Residue "A ARG 3799": "NH1" <-> "NH2" Residue "A ARG 3864": "NH1" <-> "NH2" Residue "A ARG 3889": "NH1" <-> "NH2" Residue "A GLU 3895": "OE1" <-> "OE2" Residue "A ARG 3923": "NH1" <-> "NH2" Residue "A GLU 3957": "OE1" <-> "OE2" Residue "A ARG 3962": "NH1" <-> "NH2" Residue "A ARG 3965": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C ARG 489": "NH1" <-> "NH2" Residue "C ARG 497": "NH1" <-> "NH2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 645": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 690": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 39835 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 29107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3669, 29107 Classifications: {'peptide': 3669} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 155, 'TRANS': 3512} Chain breaks: 16 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 3973 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 490, 3957 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 490, 3957 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 27, 'TRANS': 462} Chain breaks: 1 bond proxies already assigned to first conformer: 4016 Chain: "C" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5247 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 627} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 22.46, per 1000 atoms: 0.56 Number of scatterers: 39835 At special positions: 0 Unit cell: (133.4, 176.32, 241.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 233 16.00 P 71 15.00 O 7465 8.00 N 6762 7.00 C 25304 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: 15.28 Conformation dependent library (CDL) restraints added in 6.4 seconds 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9234 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 12 sheets defined 56.8% alpha, 4.1% beta 37 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 12.06 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 4.603A pdb=" N LEU A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.658A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.596A pdb=" N THR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.144A pdb=" N LEU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 removed outlier: 3.686A pdb=" N ILE A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.961A pdb=" N LEU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.564A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.454A pdb=" N SER A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.668A pdb=" N TYR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.939A pdb=" N PHE A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.731A pdb=" N LEU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.834A pdb=" N ARG A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.961A pdb=" N GLN A 281 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 328 removed outlier: 4.336A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 355 through 370 removed outlier: 4.053A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 386 through 397 removed outlier: 4.654A pdb=" N GLN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N MET A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 422 Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.149A pdb=" N HIS A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.581A pdb=" N VAL A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 526 No H-bonds generated for 'chain 'A' and resid 524 through 526' Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.729A pdb=" N PHE A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 removed outlier: 3.729A pdb=" N ASN A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) 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 645 through 658 removed outlier: 3.714A pdb=" N LEU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 680 removed outlier: 4.030A pdb=" N ILE A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 718 removed outlier: 3.792A pdb=" N LEU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 722 through 734 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.969A pdb=" N TYR A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 749 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 752 through 758 removed outlier: 3.629A pdb=" N PHE A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 780 removed outlier: 4.268A pdb=" N ALA A 766 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.745A pdb=" N CYS A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.914A pdb=" N ALA A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.955A pdb=" N LEU A 831 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 878 through 883 removed outlier: 3.871A pdb=" N TYR A 883 " --> pdb=" O MET A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 removed outlier: 4.285A pdb=" N GLU A 916 " --> pdb=" O PRO A 912 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 945 removed outlier: 3.903A pdb=" N ALA A 929 " --> pdb=" O GLN A 925 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 945 " --> pdb=" O MET A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.404A pdb=" N ARG A 964 " --> pdb=" O GLN A 960 " (cutoff:3.500A) Proline residue: A 967 - end of helix removed outlier: 3.861A pdb=" N LEU A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG A 971 " --> pdb=" O PRO A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 996 Proline residue: A 986 - end of helix removed outlier: 4.198A pdb=" N ILE A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 993 " --> pdb=" O MET A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1018 removed outlier: 3.571A pdb=" N ALA A1008 " --> pdb=" O GLN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1043 removed outlier: 3.812A pdb=" N PHE A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A1043 " --> pdb=" O TRP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1068 Processing helix chain 'A' and resid 1071 through 1074 Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.787A pdb=" N PHE A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1114 Processing helix chain 'A' and resid 1123 through 1133 removed outlier: 4.158A pdb=" N ASP A1129 " --> pdb=" O GLN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1175 Processing helix chain 'A' and resid 1180 through 1193 removed outlier: 4.127A pdb=" N HIS A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1216 removed outlier: 3.512A pdb=" N LYS A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1252 through 1267 removed outlier: 4.611A pdb=" N TYR A1267 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1277 through 1283 removed outlier: 3.586A pdb=" N VAL A1281 " --> pdb=" O GLY A1277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A1283 " --> pdb=" O LEU A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1298 removed outlier: 3.586A pdb=" N PHE A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1335 removed outlier: 4.344A pdb=" N SER A1333 " --> pdb=" O ARG A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1349 Processing helix chain 'A' and resid 1367 through 1377 removed outlier: 4.505A pdb=" N VAL A1373 " --> pdb=" O MET A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1404 Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1424 through 1432 Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 3.541A pdb=" N ALA A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.797A pdb=" N ILE A1467 " --> pdb=" O LEU A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1490 Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 3.897A pdb=" N LEU A1515 " --> pdb=" O ALA A1511 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A1516 " --> pdb=" O SER A1512 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A1518 " --> pdb=" O LEU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1556 through 1564 removed outlier: 4.327A pdb=" N PHE A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A1564 " --> pdb=" O TYR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1574 removed outlier: 3.747A pdb=" N LYS A1573 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A1574 " --> pdb=" O GLU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1585 removed outlier: 4.417A pdb=" N SER A1585 " --> pdb=" O GLU A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1607 removed outlier: 3.995A pdb=" N GLN A1603 " --> pdb=" O GLY A1599 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A1607 " --> pdb=" O GLN A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1623 removed outlier: 4.228A pdb=" N GLY A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1617 " --> pdb=" O HIS A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1629 removed outlier: 5.790A pdb=" N LYS A1627 " --> pdb=" O GLN A1624 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A1629 " --> pdb=" O TRP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1656 removed outlier: 4.340A pdb=" N LYS A1642 " --> pdb=" O PRO A1638 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A1643 " --> pdb=" O LEU A1639 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A1656 " --> pdb=" O ILE A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 3.894A pdb=" N THR A1673 " --> pdb=" O PRO A1669 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A1679 " --> pdb=" O TYR A1675 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A1681 " --> pdb=" O SER A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 3.699A pdb=" N GLY A1690 " --> pdb=" O LEU A1686 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN A1691 " --> pdb=" O HIS A1687 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A1692 " --> pdb=" O LEU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1706 through 1719 Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 3.594A pdb=" N LYS A1745 " --> pdb=" O ASP A1741 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A1752 " --> pdb=" O ASP A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1767 removed outlier: 3.717A pdb=" N MET A1762 " --> pdb=" O LEU A1758 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A1764 " --> pdb=" O GLU A1760 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A1765 " --> pdb=" O LEU A1761 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS A1767 " --> pdb=" O THR A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1787 removed outlier: 4.027A pdb=" N ARG A1787 " --> pdb=" O ARG A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1807 removed outlier: 3.977A pdb=" N GLN A1794 " --> pdb=" O SER A1790 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1830 removed outlier: 4.101A pdb=" N PHE A1819 " --> pdb=" O THR A1815 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A1820 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A1824 " --> pdb=" O VAL A1820 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1843 through 1852 removed outlier: 4.105A pdb=" N ILE A1848 " --> pdb=" O VAL A1844 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP A1849 " --> pdb=" O VAL A1845 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A1850 " --> pdb=" O ASP A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1859 through 1883 removed outlier: 4.383A pdb=" N THR A1865 " --> pdb=" O SER A1861 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A1883 " --> pdb=" O VAL A1879 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 Processing helix chain 'A' and resid 1895 through 1900 Processing helix chain 'A' and resid 1910 through 1924 removed outlier: 4.002A pdb=" N THR A1914 " --> pdb=" O GLU A1910 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A1918 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A1923 " --> pdb=" O CYS A1919 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A1924 " --> pdb=" O TYR A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1954 removed outlier: 3.524A pdb=" N LEU A1939 " --> pdb=" O GLU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1967 Processing helix chain 'A' and resid 1970 through 1974 removed outlier: 3.876A pdb=" N LYS A1973 " --> pdb=" O LYS A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1982 removed outlier: 3.624A pdb=" N LEU A1981 " --> pdb=" O ILE A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2016 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2126 through 2134 Processing helix chain 'A' and resid 2139 through 2153 removed outlier: 3.608A pdb=" N ARG A2143 " --> pdb=" O PRO A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2161 removed outlier: 3.611A pdb=" N TYR A2160 " --> pdb=" O PHE A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2174 Processing helix chain 'A' and resid 2182 through 2196 removed outlier: 4.005A pdb=" N VAL A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A2188 " --> pdb=" O TYR A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2222 Processing helix chain 'A' and resid 2227 through 2246 removed outlier: 4.043A pdb=" N LYS A2246 " --> pdb=" O VAL A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2254 through 2261 Processing helix chain 'A' and resid 2270 through 2284 removed outlier: 3.587A pdb=" N ILE A2274 " --> pdb=" O ASN A2270 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A2283 " --> pdb=" O ILE A2279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A2284 " --> pdb=" O VAL A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2308 removed outlier: 3.850A pdb=" N GLN A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A2308 " --> pdb=" O VAL A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2315 through 2333 removed outlier: 3.818A pdb=" N GLU A2332 " --> pdb=" O ARG A2328 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2356 removed outlier: 3.644A pdb=" N LEU A2341 " --> pdb=" O LEU A2337 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN A2354 " --> pdb=" O LYS A2350 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A2356 " --> pdb=" O HIS A2352 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2371 removed outlier: 3.811A pdb=" N CYS A2363 " --> pdb=" O LYS A2359 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A2370 " --> pdb=" O LYS A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2385 through 2389 removed outlier: 4.004A pdb=" N PHE A2389 " --> pdb=" O LEU A2386 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2402 removed outlier: 4.066A pdb=" N THR A2395 " --> pdb=" O GLY A2391 " (cutoff:3.500A) Processing helix chain 'A' and resid 2403 through 2405 No H-bonds generated for 'chain 'A' and resid 2403 through 2405' Processing helix chain 'A' and resid 2411 through 2418 Processing helix chain 'A' and resid 2420 through 2424 Processing helix chain 'A' and resid 2430 through 2442 removed outlier: 4.055A pdb=" N LEU A2436 " --> pdb=" O GLN A2432 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A2439 " --> pdb=" O CYS A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2455 removed outlier: 3.604A pdb=" N ARG A2452 " --> pdb=" O PRO A2448 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A2453 " --> pdb=" O VAL A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2483 removed outlier: 3.536A pdb=" N ARG A2470 " --> pdb=" O SER A2466 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A2478 " --> pdb=" O TYR A2474 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP A2479 " --> pdb=" O ASN A2475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A2482 " --> pdb=" O MET A2478 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2503 Processing helix chain 'A' and resid 2507 through 2511 removed outlier: 3.841A pdb=" N ILE A2511 " --> pdb=" O GLN A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2516 through 2526 Processing helix chain 'A' and resid 2534 through 2542 Processing helix chain 'A' and resid 2553 through 2565 removed outlier: 4.351A pdb=" N MET A2565 " --> pdb=" O PHE A2561 " (cutoff:3.500A) Processing helix chain 'A' and resid 2786 through 2790 Processing helix chain 'A' and resid 2791 through 2799 Processing helix chain 'A' and resid 2801 through 2820 removed outlier: 3.529A pdb=" N ALA A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A2814 " --> pdb=" O SER A2810 " (cutoff:3.500A) Processing helix chain 'A' and resid 2825 through 2847 removed outlier: 4.486A pdb=" N ASN A2831 " --> pdb=" O SER A2827 " (cutoff:3.500A) Processing helix chain 'A' and resid 2851 through 2863 removed outlier: 4.299A pdb=" N CYS A2857 " --> pdb=" O PRO A2853 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A2859 " --> pdb=" O VAL A2855 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A2860 " --> pdb=" O SER A2856 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS A2863 " --> pdb=" O GLN A2859 " (cutoff:3.500A) Processing helix chain 'A' and resid 2874 through 2881 removed outlier: 4.046A pdb=" N ALA A2878 " --> pdb=" O ALA A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2885 through 2897 removed outlier: 3.822A pdb=" N GLY A2889 " --> pdb=" O GLN A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2931 removed outlier: 3.560A pdb=" N TRP A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) Processing helix chain 'A' and resid 2951 through 2958 removed outlier: 4.024A pdb=" N SER A2955 " --> pdb=" O GLN A2951 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2977 Processing helix chain 'A' and resid 2987 through 3004 Processing helix chain 'A' and resid 3009 through 3017 Processing helix chain 'A' and resid 3036 through 3053 removed outlier: 3.811A pdb=" N LEU A3041 " --> pdb=" O GLN A3037 " (cutoff:3.500A) Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3061 through 3069 Processing helix chain 'A' and resid 3076 through 3081 removed outlier: 3.753A pdb=" N HIS A3081 " --> pdb=" O ILE A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3083 through 3091 Processing helix chain 'A' and resid 3097 through 3115 removed outlier: 3.620A pdb=" N TYR A3101 " --> pdb=" O ASP A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3130 Processing helix chain 'A' and resid 3131 through 3147 removed outlier: 3.660A pdb=" N SER A3146 " --> pdb=" O ILE A3142 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A3147 " --> pdb=" O SER A3143 " (cutoff:3.500A) Processing helix chain 'A' and resid 3154 through 3165 removed outlier: 3.908A pdb=" N ARG A3159 " --> pdb=" O VAL A3155 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A3165 " --> pdb=" O LEU A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3197 removed outlier: 3.581A pdb=" N TRP A3179 " --> pdb=" O PRO A3175 " (cutoff:3.500A) Processing helix chain 'A' and resid 3227 through 3231 removed outlier: 3.891A pdb=" N ILE A3231 " --> pdb=" O ILE A3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3227 through 3231' Processing helix chain 'A' and resid 3231 through 3249 removed outlier: 4.451A pdb=" N SER A3237 " --> pdb=" O SER A3233 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A3241 " --> pdb=" O SER A3237 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A3248 " --> pdb=" O ASP A3244 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A3249 " --> pdb=" O SER A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3262 removed outlier: 3.592A pdb=" N ALA A3255 " --> pdb=" O ASN A3251 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A3257 " --> pdb=" O SER A3253 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3269 removed outlier: 3.546A pdb=" N THR A3268 " --> pdb=" O GLU A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3272 through 3288 removed outlier: 3.640A pdb=" N HIS A3285 " --> pdb=" O CYS A3281 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A3288 " --> pdb=" O SER A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3303 Processing helix chain 'A' and resid 3320 through 3341 removed outlier: 3.707A pdb=" N GLN A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A3327 " --> pdb=" O PHE A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3346 through 3350 removed outlier: 3.824A pdb=" N ALA A3349 " --> pdb=" O ALA A3346 " (cutoff:3.500A) Processing helix chain 'A' and resid 3354 through 3361 Processing helix chain 'A' and resid 3371 through 3394 removed outlier: 4.824A pdb=" N LEU A3377 " --> pdb=" O VAL A3373 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A3388 " --> pdb=" O HIS A3384 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A3389 " --> pdb=" O LEU A3385 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN A3390 " --> pdb=" O SER A3386 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A3394 " --> pdb=" O GLN A3390 " (cutoff:3.500A) Processing helix chain 'A' and resid 3409 through 3429 removed outlier: 3.663A pdb=" N LEU A3416 " --> pdb=" O ALA A3412 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A3429 " --> pdb=" O ARG A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3433 through 3440 Processing helix chain 'A' and resid 3441 through 3456 removed outlier: 3.803A pdb=" N VAL A3447 " --> pdb=" O PRO A3443 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A3448 " --> pdb=" O ALA A3444 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A3449 " --> pdb=" O LEU A3445 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A3453 " --> pdb=" O LYS A3449 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A3455 " --> pdb=" O LEU A3451 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) Processing helix chain 'A' and resid 3461 through 3463 No H-bonds generated for 'chain 'A' and resid 3461 through 3463' Processing helix chain 'A' and resid 3464 through 3475 removed outlier: 3.825A pdb=" N LEU A3468 " --> pdb=" O LYS A3464 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3480 through 3488 removed outlier: 4.049A pdb=" N GLU A3486 " --> pdb=" O LEU A3482 " (cutoff:3.500A) Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3514 through 3525 Processing helix chain 'A' and resid 3530 through 3538 removed outlier: 3.733A pdb=" N ILE A3534 " --> pdb=" O VAL A3530 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A3535 " --> pdb=" O TYR A3531 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A3536 " --> pdb=" O PRO A3532 " (cutoff:3.500A) Processing helix chain 'A' and resid 3547 through 3562 Processing helix chain 'A' and resid 3567 through 3577 Processing helix chain 'A' and resid 3580 through 3594 removed outlier: 4.170A pdb=" N LEU A3584 " --> pdb=" O ASN A3580 " (cutoff:3.500A) Processing helix chain 'A' and resid 3604 through 3616 removed outlier: 4.382A pdb=" N GLU A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A3612 " --> pdb=" O LYS A3608 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A3613 " --> pdb=" O MET A3609 " (cutoff:3.500A) Processing helix chain 'A' and resid 3620 through 3627 removed outlier: 4.174A pdb=" N GLY A3624 " --> pdb=" O PRO A3620 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3637 Processing helix chain 'A' and resid 3641 through 3651 removed outlier: 4.038A pdb=" N LYS A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A3647 " --> pdb=" O HIS A3643 " (cutoff:3.500A) Processing helix chain 'A' and resid 3660 through 3670 removed outlier: 4.359A pdb=" N LEU A3666 " --> pdb=" O ILE A3662 " (cutoff:3.500A) Processing helix chain 'A' and resid 3758 through 3776 removed outlier: 3.744A pdb=" N GLN A3762 " --> pdb=" O LEU A3758 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A3776 " --> pdb=" O ASN A3772 " (cutoff:3.500A) Processing helix chain 'A' and resid 3778 through 3783 removed outlier: 3.501A pdb=" N SER A3782 " --> pdb=" O ASP A3778 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A3783 " --> pdb=" O SER A3779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3778 through 3783' Processing helix chain 'A' and resid 3812 through 3820 Processing helix chain 'A' and resid 3821 through 3830 removed outlier: 4.494A pdb=" N ALA A3826 " --> pdb=" O GLN A3822 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A3827 " --> pdb=" O GLU A3823 " (cutoff:3.500A) Processing helix chain 'A' and resid 3834 through 3848 removed outlier: 3.884A pdb=" N TYR A3839 " --> pdb=" O PRO A3835 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A3840 " --> pdb=" O PRO A3836 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A3847 " --> pdb=" O LEU A3843 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 removed outlier: 3.690A pdb=" N TYR A3859 " --> pdb=" O TYR A3855 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A3860 " --> pdb=" O MET A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3863 through 3876 removed outlier: 3.804A pdb=" N THR A3867 " --> pdb=" O ASN A3863 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A3868 " --> pdb=" O ARG A3864 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR A3869 " --> pdb=" O THR A3865 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A3873 " --> pdb=" O THR A3869 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A3874 " --> pdb=" O SER A3870 " (cutoff:3.500A) Processing helix chain 'A' and resid 3882 through 3889 Processing helix chain 'A' and resid 3893 through 3918 removed outlier: 4.169A pdb=" N LEU A3898 " --> pdb=" O PRO A3894 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A3899 " --> pdb=" O GLU A3895 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A3903 " --> pdb=" O ALA A3899 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP A3916 " --> pdb=" O CYS A3912 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A3917 " --> pdb=" O ILE A3913 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A3918 " --> pdb=" O SER A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3965 through 3970 Processing helix chain 'A' and resid 3978 through 3992 removed outlier: 3.994A pdb=" N SER A3982 " --> pdb=" O GLY A3978 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A3983 " --> pdb=" O LEU A3979 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N MET A3984 " --> pdb=" O MET A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3996 through 4002 Processing helix chain 'A' and resid 4003 through 4008 Processing helix chain 'A' and resid 4016 through 4023 Processing helix chain 'A' and resid 4039 through 4053 Processing helix chain 'A' and resid 4057 through 4069 removed outlier: 3.847A pdb=" N LEU A4064 " --> pdb=" O THR A4060 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A4067 " --> pdb=" O GLU A4063 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 Processing helix chain 'A' and resid 4088 through 4092 removed outlier: 3.723A pdb=" N ALA A4091 " --> pdb=" O ASN A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4112 Processing helix chain 'A' and resid 4113 through 4119 removed outlier: 4.175A pdb=" N ARG A4119 " --> pdb=" O ASN A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 78 removed outlier: 4.373A pdb=" N ILE B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.701A pdb=" N ASP B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.797A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.240A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 Processing helix chain 'B' and resid 511 through 519 removed outlier: 3.917A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'C' and resid 29 through 48 Processing helix chain 'C' and resid 88 through 96 removed outlier: 4.237A pdb=" N ILE C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 removed outlier: 4.061A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.554A pdb=" N ASP C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.021A pdb=" N GLU C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 484 through 500 removed outlier: 4.122A pdb=" N GLN C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 516 removed outlier: 3.940A pdb=" N TRP C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.571A pdb=" N PHE C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 605 removed outlier: 3.743A pdb=" N LYS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 626 Processing helix chain 'C' and resid 628 through 649 removed outlier: 3.690A pdb=" N PHE C 632 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET C 633 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 644 " --> pdb=" O ARG C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 669 Processing helix chain 'C' and resid 671 through 680 Processing helix chain 'C' and resid 698 through 705 Processing sheet with id=AA1, first strand: chain 'A' and resid 893 through 894 Processing sheet with id=AA2, first strand: chain 'A' and resid 3727 through 3728 removed outlier: 6.899A pdb=" N LEU A3802 " --> pdb=" O PRO A3795 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU A3804 " --> pdb=" O VAL A3793 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A3793 " --> pdb=" O GLU A3804 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3809 through 3811 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.622A pdb=" N ASP B 36 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ALA B 84 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 38 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR B 88 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 42 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ARG B 35 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG B 165 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER B 37 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET B 167 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 39 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE B 169 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 41 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N PHE B 199 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 164 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP B 201 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 166 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET B 203 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 168 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 272 removed outlier: 5.492A pdb=" N LEU B 345 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR B 401 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 347 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG B 399 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 349 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL B 394 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 298 through 303 Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.963A pdb=" N ARG B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 318 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 84 removed outlier: 7.144A pdb=" N HIS C 80 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N LEU C 58 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS C 82 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU C 56 " --> pdb=" O HIS C 82 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA C 8 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 55 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 10 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL C 57 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 12 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE C 59 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET C 14 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 9 " --> pdb=" O HIS C 131 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLU C 133 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 11 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE C 135 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS C 13 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 130 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN C 162 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 132 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE C 164 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 134 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR C 225 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 163 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 247 through 253 removed outlier: 6.585A pdb=" N TYR C 264 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 364 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 339 through 346 removed outlier: 3.764A pdb=" N CYS C 339 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE C 392 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE C 345 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 390 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 464 through 466 1627 hydrogen bonds defined for protein. 4793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 26.52 Time building geometry restraints manager: 16.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7444 1.32 - 1.45: 10025 1.45 - 1.57: 22812 1.57 - 1.70: 142 1.70 - 1.82: 368 Bond restraints: 40791 Sorted by residual: bond pdb=" CG ASN A 356 " pdb=" OD1 ASN A 356 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.60e+01 bond pdb=" CG ASN A 356 " pdb=" ND2 ASN A 356 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.20e+01 bond pdb=" CA LEU B 337 " pdb=" C LEU B 337 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.34e-02 5.57e+03 1.52e+01 bond pdb=" N LYS A2824 " pdb=" CA LYS A2824 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.79e+00 bond pdb=" C LEU A 217 " pdb=" N PRO A 218 " ideal model delta sigma weight residual 1.334 1.360 -0.026 8.40e-03 1.42e+04 9.70e+00 ... (remaining 40786 not shown) Histogram of bond angle deviations from ideal: 93.68 - 103.73: 799 103.73 - 113.78: 23564 113.78 - 123.84: 29587 123.84 - 133.89: 1430 133.89 - 143.94: 51 Bond angle restraints: 55431 Sorted by residual: angle pdb=" C LEU A2122 " pdb=" N PRO A2123 " pdb=" CA PRO A2123 " ideal model delta sigma weight residual 119.84 138.80 -18.96 1.25e+00 6.40e-01 2.30e+02 angle pdb=" C GLU A3895 " pdb=" CA GLU A3895 " pdb=" CB GLU A3895 " ideal model delta sigma weight residual 110.90 127.15 -16.25 1.58e+00 4.01e-01 1.06e+02 angle pdb=" C TYR B 530 " pdb=" N PRO B 531 " pdb=" CA PRO B 531 " ideal model delta sigma weight residual 120.38 110.00 10.38 1.03e+00 9.43e-01 1.01e+02 angle pdb=" N VAL A1773 " pdb=" CA VAL A1773 " pdb=" C VAL A1773 " ideal model delta sigma weight residual 113.42 102.35 11.07 1.17e+00 7.31e-01 8.95e+01 angle pdb=" C LYS A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta sigma weight residual 119.84 130.89 -11.05 1.25e+00 6.40e-01 7.81e+01 ... (remaining 55426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 20870 17.69 - 35.38: 2851 35.38 - 53.07: 750 53.07 - 70.76: 134 70.76 - 88.45: 49 Dihedral angle restraints: 24654 sinusoidal: 10488 harmonic: 14166 Sorted by residual: dihedral pdb=" C GLU A3895 " pdb=" N GLU A3895 " pdb=" CA GLU A3895 " pdb=" CB GLU A3895 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA PRO A 473 " pdb=" C PRO A 473 " pdb=" N VAL A 474 " pdb=" CA VAL A 474 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA LEU A1165 " pdb=" C LEU A1165 " pdb=" N LEU A1166 " pdb=" CA LEU A1166 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 24651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5491 0.093 - 0.186: 731 0.186 - 0.279: 67 0.279 - 0.372: 2 0.372 - 0.465: 2 Chirality restraints: 6293 Sorted by residual: chirality pdb=" CA PRO A2887 " pdb=" N PRO A2887 " pdb=" C PRO A2887 " pdb=" CB PRO A2887 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA GLU A3895 " pdb=" N GLU A3895 " pdb=" C GLU A3895 " pdb=" CB GLU A3895 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA PRO A3894 " pdb=" N PRO A3894 " pdb=" C PRO A3894 " pdb=" CB PRO A3894 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 6290 not shown) Planarity restraints: 6795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A2572 " 0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C TYR A2572 " -0.097 2.00e-02 2.50e+03 pdb=" O TYR A2572 " 0.037 2.00e-02 2.50e+03 pdb=" N PRO A2573 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1727 " -0.487 9.50e-02 1.11e+02 2.18e-01 2.91e+01 pdb=" NE ARG A1727 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A1727 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A1727 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1727 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A3835 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO A3836 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A3836 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A3836 " 0.058 5.00e-02 4.00e+02 ... (remaining 6792 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 253 2.49 - 3.09: 26171 3.09 - 3.70: 59710 3.70 - 4.30: 80483 4.30 - 4.90: 132938 Nonbonded interactions: 299555 Sorted by model distance: nonbonded pdb=" O ASN A3697 " pdb=" O GLU A3698 " model vdw 1.890 3.040 nonbonded pdb=" O GLN A1771 " pdb=" O HIS A1772 " model vdw 1.897 3.040 nonbonded pdb=" O LYS B 245 " pdb=" CG2 VAL B 246 " model vdw 2.038 3.460 nonbonded pdb=" O TYR B 530 " pdb=" O PRO B 531 " model vdw 2.107 3.040 nonbonded pdb=" O SER A 842 " pdb=" OG SER A 842 " model vdw 2.188 2.440 ... (remaining 299550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and resid 4 through 24) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 13.070 Check model and map are aligned: 0.640 Set scattering table: 0.360 Process input model: 118.570 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.009 0.113 40791 Z= 0.580 Angle : 1.180 23.232 55431 Z= 0.632 Chirality : 0.064 0.465 6293 Planarity : 0.009 0.218 6795 Dihedral : 17.538 88.454 15420 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.90 % Favored : 84.58 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.09), residues: 4768 helix: -3.09 (0.07), residues: 2631 sheet: -2.46 (0.33), residues: 202 loop : -4.40 (0.11), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 535 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 21 residues processed: 581 average time/residue: 0.5501 time to fit residues: 518.9178 Evaluate side-chains 391 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 370 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.3685 time to fit residues: 20.9479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 410 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 380 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 231 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 109 ASN A 325 ASN A 344 GLN A 437 HIS A 454 GLN A 833 HIS A 982 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN A1142 HIS A1146 ASN A1175 HIS A1280 GLN A1457 GLN A1459 HIS A1589 ASN A1598 ASN A1624 GLN A1738 ASN ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2016 ASN A2177 ASN A2270 ASN A2348 GLN A2365 ASN A2514 ASN ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2795 GLN A2799 GLN A2885 GLN A2886 GLN A2954 GLN A3113 ASN A3122 HIS ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3459 ASN A3510 GLN A3524 ASN A3564 GLN A3569 GLN A3573 ASN A3671 ASN ** A3704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 360 HIS B 423 GLN B 515 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 290 GLN C 360 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 GLN C 496 HIS ** C 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 ASN ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 40791 Z= 0.215 Angle : 0.711 21.780 55431 Z= 0.362 Chirality : 0.043 0.224 6293 Planarity : 0.006 0.081 6795 Dihedral : 13.540 73.573 5883 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.48 % Favored : 87.33 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -4.07 (0.11), residues: 4768 helix: -1.72 (0.09), residues: 2662 sheet: -2.19 (0.33), residues: 212 loop : -4.23 (0.11), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 430 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 52 residues processed: 502 average time/residue: 0.5299 time to fit residues: 448.1402 Evaluate side-chains 429 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 377 time to evaluate : 4.417 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3670 time to fit residues: 42.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 121 optimal weight: 0.0980 chunk 442 optimal weight: 2.9990 chunk 477 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 354 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3113 ASN A3459 ASN A3605 ASN A3743 HIS A3769 GLN B 359 HIS ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 40791 Z= 0.199 Angle : 0.677 21.750 55431 Z= 0.340 Chirality : 0.042 0.239 6293 Planarity : 0.005 0.068 6795 Dihedral : 13.324 75.373 5883 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.90 % Favored : 86.91 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -3.40 (0.11), residues: 4768 helix: -1.09 (0.10), residues: 2666 sheet: -1.87 (0.35), residues: 200 loop : -4.08 (0.12), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 410 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 55 residues processed: 490 average time/residue: 0.5138 time to fit residues: 428.4083 Evaluate side-chains 428 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 373 time to evaluate : 4.583 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.3969 time to fit residues: 46.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 436 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 443 optimal weight: 2.9990 chunk 469 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 420 optimal weight: 20.0000 chunk 126 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 GLN ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 GLN ** A1890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1926 ASN ** A1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 ASN A3748 HIS A3760 GLN A3787 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 40791 Z= 0.240 Angle : 0.677 21.367 55431 Z= 0.342 Chirality : 0.043 0.258 6293 Planarity : 0.005 0.066 6795 Dihedral : 13.296 74.071 5883 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.34 % Favored : 86.49 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.12), residues: 4768 helix: -0.84 (0.10), residues: 2656 sheet: -1.76 (0.36), residues: 198 loop : -4.02 (0.12), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 393 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 43 residues processed: 460 average time/residue: 0.5264 time to fit residues: 413.2593 Evaluate side-chains 406 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 363 time to evaluate : 4.758 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4059 time to fit residues: 40.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 391 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 349 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 400 optimal weight: 0.0020 chunk 324 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 421 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1779 GLN ** A1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3927 ASN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 40791 Z= 0.181 Angle : 0.644 21.395 55431 Z= 0.322 Chirality : 0.041 0.250 6293 Planarity : 0.004 0.064 6795 Dihedral : 13.144 70.666 5883 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.15 % Favored : 87.70 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.12), residues: 4768 helix: -0.55 (0.10), residues: 2644 sheet: -1.57 (0.37), residues: 200 loop : -3.88 (0.12), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 409 time to evaluate : 4.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 27 residues processed: 459 average time/residue: 0.5313 time to fit residues: 417.4726 Evaluate side-chains 398 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 371 time to evaluate : 5.100 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4160 time to fit residues: 28.1858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 158 optimal weight: 7.9990 chunk 423 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 chunk 390 optimal weight: 0.0980 chunk 217 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 155 optimal weight: 1.9990 chunk 246 optimal weight: 0.1980 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2865 HIS A3769 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 40791 Z= 0.160 Angle : 0.629 20.604 55431 Z= 0.313 Chirality : 0.040 0.231 6293 Planarity : 0.004 0.061 6795 Dihedral : 12.999 68.043 5883 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.64 % Favored : 88.23 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.12), residues: 4768 helix: -0.27 (0.10), residues: 2644 sheet: -1.44 (0.37), residues: 200 loop : -3.76 (0.12), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9536 Ramachandran restraints generated. 4768 Oldfield, 0 Emsley, 4768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 415 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 446 average time/residue: 0.5307 time to fit residues: 405.1427 Evaluate side-chains 398 residues out of total 4309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 378 time to evaluate : 4.591 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4018 time to fit residues: 21.3207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 453 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 395 optimal weight: 2.9990 chunk 262 optimal weight: 0.0980 chunk 468 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: