Starting phenix.real_space_refine on Tue Apr 16 19:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anw_11834/04_2024/7anw_11834_updated.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.029 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 16 5.49 5 S 192 5.16 5 C 25496 2.51 5 N 7264 2.21 5 O 7552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D GLU 693": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 431": "OE1" <-> "OE2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ARG 463": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E GLU 670": "OE1" <-> "OE2" Residue "E GLU 693": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F GLU 286": "OE1" <-> "OE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "F ARG 445": "NH1" <-> "NH2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F ARG 463": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ARG 537": "NH1" <-> "NH2" Residue "F GLU 670": "OE1" <-> "OE2" Residue "F GLU 693": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 395": "NH1" <-> "NH2" Residue "G TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G GLU 450": "OE1" <-> "OE2" Residue "G ARG 463": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "G GLU 525": "OE1" <-> "OE2" Residue "G ARG 537": "NH1" <-> "NH2" Residue "G GLU 670": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H GLU 286": "OE1" <-> "OE2" Residue "H PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "H ARG 445": "NH1" <-> "NH2" Residue "H GLU 450": "OE1" <-> "OE2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Residue "H GLU 525": "OE1" <-> "OE2" Residue "H ARG 537": "NH1" <-> "NH2" Residue "H GLU 670": "OE1" <-> "OE2" Residue "H GLU 693": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "C" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "D" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "E" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "F" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "G" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "H" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.51, per 1000 atoms: 0.48 Number of scatterers: 40520 At special positions: 0 Unit cell: (210.885, 210.885, 84.354, 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 192 16.00 P 16 15.00 O 7552 8.00 N 7264 7.00 C 25496 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: 15.41 Conformation dependent library (CDL) restraints added in 6.9 seconds 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 304 helices and 8 sheets defined 58.9% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.32 Creating SS restraints... Processing helix chain 'A' and resid 57 through 78 removed outlier: 3.690A pdb=" N ARG A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.781A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 220 through 236 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.584A pdb=" N VAL A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.558A pdb=" N ALA A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.990A pdb=" N ARG A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.703A pdb=" N LEU A 491 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 492 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 removed outlier: 4.466A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.831A pdb=" N LEU A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 670 through 677 removed outlier: 4.346A pdb=" N ALA A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 670 through 677' Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 78 removed outlier: 3.690A pdb=" N ARG B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.780A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 220 through 236 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 251 through 258 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Proline residue: B 298 - end of helix removed outlier: 3.557A pdb=" N ALA B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.991A pdb=" N ARG B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU B 491 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY B 492 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 506 removed outlier: 4.465A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 517 removed outlier: 3.829A pdb=" N LEU B 515 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 512 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 665 through 667 No H-bonds generated for 'chain 'B' and resid 665 through 667' Processing helix chain 'B' and resid 670 through 677 removed outlier: 4.346A pdb=" N ALA B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU B 676 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 670 through 677' Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.652A pdb=" N PHE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 78 removed outlier: 3.689A pdb=" N ARG C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 178 through 191 removed outlier: 3.781A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 220 through 236 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 251 through 258 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Proline residue: C 298 - end of helix removed outlier: 3.557A pdb=" N ALA C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 339 through 359 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.991A pdb=" N ARG C 376 " --> pdb=" O GLN C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 475 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU C 491 " --> pdb=" O ALA C 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY C 492 " --> pdb=" O ASP C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 506 removed outlier: 4.465A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.830A pdb=" N LEU C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 512 through 517' Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 670 through 677 removed outlier: 4.346A pdb=" N ALA C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU C 676 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C 677 " --> pdb=" O GLN C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 677' Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 78 removed outlier: 3.690A pdb=" N ARG D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.780A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 208 through 211 No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 220 through 236 Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 251 through 258 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.519A pdb=" N ARG D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.557A pdb=" N ALA D 301 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 339 through 359 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.990A pdb=" N ARG D 376 " --> pdb=" O GLN D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 462 through 476 removed outlier: 3.551A pdb=" N ARG D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 475 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 494 removed outlier: 3.703A pdb=" N LEU D 491 " --> pdb=" O ALA D 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY D 492 " --> pdb=" O ASP D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 506 removed outlier: 4.465A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.831A pdb=" N LEU D 515 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 517' Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 586 Processing helix chain 'D' and resid 606 through 613 Processing helix chain 'D' and resid 638 through 649 Processing helix chain 'D' and resid 665 through 667 No H-bonds generated for 'chain 'D' and resid 665 through 667' Processing helix chain 'D' and resid 670 through 677 removed outlier: 4.347A pdb=" N ALA D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR D 677 " --> pdb=" O GLN D 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 670 through 677' Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 78 removed outlier: 3.689A pdb=" N ARG E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.597A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 Processing helix chain 'E' and resid 165 through 171 Processing helix chain 'E' and resid 178 through 191 removed outlier: 3.781A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 251 through 258 Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Proline residue: E 298 - end of helix removed outlier: 3.558A pdb=" N ALA E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 339 through 359 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 371 through 376 removed outlier: 3.990A pdb=" N ARG E 376 " --> pdb=" O GLN E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'E' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG E 468 " --> pdb=" O LYS E 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU E 491 " --> pdb=" O ALA E 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY E 492 " --> pdb=" O ASP E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 506 removed outlier: 4.464A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 517 removed outlier: 3.830A pdb=" N LEU E 515 " --> pdb=" O ARG E 512 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 512 through 517' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU E 544 " --> pdb=" O THR E 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 546 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 586 Processing helix chain 'E' and resid 606 through 613 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' Processing helix chain 'E' and resid 670 through 677 removed outlier: 4.346A pdb=" N ALA E 674 " --> pdb=" O GLU E 670 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU E 676 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR E 677 " --> pdb=" O GLN E 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 670 through 677' Processing helix chain 'E' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE E 698 " --> pdb=" O LYS E 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 78 removed outlier: 3.690A pdb=" N ARG F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 165 through 171 Processing helix chain 'F' and resid 178 through 191 removed outlier: 3.780A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 208 through 211 No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 220 through 236 Processing helix chain 'F' and resid 238 through 247 Processing helix chain 'F' and resid 251 through 258 Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Proline residue: F 298 - end of helix removed outlier: 3.558A pdb=" N ALA F 301 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 339 through 359 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 371 through 376 removed outlier: 3.991A pdb=" N ARG F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 414 through 423 Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG F 468 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 475 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU F 491 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY F 492 " --> pdb=" O ASP F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 506 removed outlier: 4.465A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 517 removed outlier: 3.831A pdb=" N LEU F 515 " --> pdb=" O ARG F 512 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 512 through 517' Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU F 544 " --> pdb=" O THR F 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS F 547 " --> pdb=" O ARG F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 586 Processing helix chain 'F' and resid 606 through 613 Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 665 through 667 No H-bonds generated for 'chain 'F' and resid 665 through 667' Processing helix chain 'F' and resid 670 through 677 removed outlier: 4.347A pdb=" N ALA F 674 " --> pdb=" O GLU F 670 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU F 676 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR F 677 " --> pdb=" O GLN F 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 670 through 677' Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE F 698 " --> pdb=" O LYS F 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 78 removed outlier: 3.690A pdb=" N ARG G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'G' and resid 178 through 191 removed outlier: 3.780A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 208 through 211 No H-bonds generated for 'chain 'G' and resid 208 through 211' Processing helix chain 'G' and resid 220 through 236 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 251 through 258 Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 290 removed outlier: 3.518A pdb=" N ARG G 289 " --> pdb=" O ARG G 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU G 297 " --> pdb=" O ALA G 294 " (cutoff:3.500A) Proline residue: G 298 - end of helix removed outlier: 3.557A pdb=" N ALA G 301 " --> pdb=" O PRO G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 339 through 359 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 371 through 376 removed outlier: 3.990A pdb=" N ARG G 376 " --> pdb=" O GLN G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 396 Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 430 through 435 Processing helix chain 'G' and resid 440 through 443 No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 448 through 453 Processing helix chain 'G' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG G 468 " --> pdb=" O LYS G 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 475 " --> pdb=" O THR G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU G 491 " --> pdb=" O ALA G 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY G 492 " --> pdb=" O ASP G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 506 removed outlier: 4.464A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.830A pdb=" N LEU G 515 " --> pdb=" O ARG G 512 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 512 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 546 " --> pdb=" O ALA G 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS G 547 " --> pdb=" O ARG G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 586 Processing helix chain 'G' and resid 606 through 613 Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 665 through 667 No H-bonds generated for 'chain 'G' and resid 665 through 667' Processing helix chain 'G' and resid 670 through 677 removed outlier: 4.346A pdb=" N ALA G 674 " --> pdb=" O GLU G 670 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL G 675 " --> pdb=" O ASP G 671 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU G 676 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR G 677 " --> pdb=" O GLN G 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 670 through 677' Processing helix chain 'G' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE G 698 " --> pdb=" O LYS G 694 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 78 removed outlier: 3.689A pdb=" N ARG H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.654A pdb=" N ALA H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 138 through 151 removed outlier: 3.599A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 165 through 171 Processing helix chain 'H' and resid 178 through 191 removed outlier: 3.780A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 211 No H-bonds generated for 'chain 'H' and resid 208 through 211' Processing helix chain 'H' and resid 220 through 236 Processing helix chain 'H' and resid 238 through 247 Processing helix chain 'H' and resid 251 through 258 Proline residue: H 256 - end of helix Processing helix chain 'H' and resid 265 through 279 removed outlier: 3.585A pdb=" N VAL H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 279 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 removed outlier: 3.519A pdb=" N ARG H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 302 removed outlier: 4.123A pdb=" N GLU H 297 " --> pdb=" O ALA H 294 " (cutoff:3.500A) Proline residue: H 298 - end of helix removed outlier: 3.557A pdb=" N ALA H 301 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 339 through 359 Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 371 through 376 removed outlier: 3.991A pdb=" N ARG H 376 " --> pdb=" O GLN H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 396 Processing helix chain 'H' and resid 409 through 411 No H-bonds generated for 'chain 'H' and resid 409 through 411' Processing helix chain 'H' and resid 414 through 423 Processing helix chain 'H' and resid 430 through 435 Processing helix chain 'H' and resid 440 through 443 No H-bonds generated for 'chain 'H' and resid 440 through 443' Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 462 through 476 removed outlier: 3.550A pdb=" N ARG H 468 " --> pdb=" O LYS H 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 475 " --> pdb=" O THR H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 494 removed outlier: 3.702A pdb=" N LEU H 491 " --> pdb=" O ALA H 488 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY H 492 " --> pdb=" O ASP H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 506 removed outlier: 4.465A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 517 removed outlier: 3.831A pdb=" N LEU H 515 " --> pdb=" O ARG H 512 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N HIS H 516 " --> pdb=" O SER H 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 512 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 547 removed outlier: 3.569A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 546 " --> pdb=" O ALA H 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS H 547 " --> pdb=" O ARG H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 586 Processing helix chain 'H' and resid 606 through 613 Processing helix chain 'H' and resid 638 through 649 Processing helix chain 'H' and resid 665 through 667 No H-bonds generated for 'chain 'H' and resid 665 through 667' Processing helix chain 'H' and resid 670 through 677 removed outlier: 4.347A pdb=" N ALA H 674 " --> pdb=" O GLU H 670 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL H 675 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU H 676 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR H 677 " --> pdb=" O GLN H 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 670 through 677' Processing helix chain 'H' and resid 688 through 698 removed outlier: 3.651A pdb=" N PHE H 698 " --> pdb=" O LYS H 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN A 616 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER A 567 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 618 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN A 652 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU A 619 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 654 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 621 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 656 " --> pdb=" O LEU A 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN B 652 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 619 " --> pdb=" O ASN B 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 654 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 621 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE B 656 " --> pdb=" O LEU B 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C 616 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER C 567 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 618 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN C 652 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 619 " --> pdb=" O ASN C 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 654 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU C 621 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 656 " --> pdb=" O LEU C 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN D 616 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER D 567 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 618 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN D 652 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 619 " --> pdb=" O ASN D 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 654 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU D 621 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE D 656 " --> pdb=" O LEU D 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN E 616 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER E 567 " --> pdb=" O ASN E 616 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL E 618 " --> pdb=" O SER E 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN E 652 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU E 619 " --> pdb=" O ASN E 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL E 654 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU E 621 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE E 656 " --> pdb=" O LEU E 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN F 616 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER F 567 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 618 " --> pdb=" O SER F 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN F 652 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU F 619 " --> pdb=" O ASN F 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 654 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU F 621 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE F 656 " --> pdb=" O LEU F 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'G' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN G 616 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER G 567 " --> pdb=" O ASN G 616 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL G 618 " --> pdb=" O SER G 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN G 652 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU G 619 " --> pdb=" O ASN G 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL G 654 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU G 621 " --> pdb=" O VAL G 654 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE G 656 " --> pdb=" O LEU G 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN H 616 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER H 567 " --> pdb=" O ASN H 616 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL H 618 " --> pdb=" O SER H 567 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN H 652 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU H 619 " --> pdb=" O ASN H 652 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL H 654 " --> pdb=" O LEU H 619 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU H 621 " --> pdb=" O VAL H 654 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE H 656 " --> pdb=" O LEU H 621 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1568 hydrogen bonds defined for protein. 4440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.27 Time building geometry restraints manager: 16.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9060 1.33 - 1.45: 11270 1.45 - 1.58: 20621 1.58 - 1.71: 33 1.71 - 1.83: 248 Bond restraints: 41232 Sorted by residual: bond pdb=" CD ARG A 484 " pdb=" NE ARG A 484 " ideal model delta sigma weight residual 1.458 1.590 -0.132 1.40e-02 5.10e+03 8.83e+01 bond pdb=" CG ARG A 484 " pdb=" CD ARG A 484 " ideal model delta sigma weight residual 1.520 1.305 0.215 3.00e-02 1.11e+03 5.14e+01 bond pdb=" CA SER E 381 " pdb=" CB SER E 381 " ideal model delta sigma weight residual 1.530 1.460 0.069 1.55e-02 4.16e+03 2.00e+01 bond pdb=" CA SER H 381 " pdb=" CB SER H 381 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.55e-02 4.16e+03 1.98e+01 bond pdb=" CA SER B 381 " pdb=" CB SER B 381 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.55e-02 4.16e+03 1.98e+01 ... (remaining 41227 not shown) Histogram of bond angle deviations from ideal: 94.60 - 102.61: 389 102.61 - 110.63: 11310 110.63 - 118.64: 22794 118.64 - 126.66: 20830 126.66 - 134.67: 509 Bond angle restraints: 55832 Sorted by residual: angle pdb=" C LYS E 375 " pdb=" CA LYS E 375 " pdb=" CB LYS E 375 " ideal model delta sigma weight residual 111.22 99.77 11.45 1.23e+00 6.61e-01 8.66e+01 angle pdb=" C LYS D 375 " pdb=" CA LYS D 375 " pdb=" CB LYS D 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS B 375 " pdb=" CA LYS B 375 " pdb=" CB LYS B 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS F 375 " pdb=" CA LYS F 375 " pdb=" CB LYS F 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS A 375 " pdb=" CA LYS A 375 " pdb=" CB LYS A 375 " ideal model delta sigma weight residual 111.22 99.80 11.42 1.23e+00 6.61e-01 8.62e+01 ... (remaining 55827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 21845 19.78 - 39.56: 2627 39.56 - 59.35: 576 59.35 - 79.13: 200 79.13 - 98.91: 96 Dihedral angle restraints: 25344 sinusoidal: 10552 harmonic: 14792 Sorted by residual: dihedral pdb=" C LYS E 375 " pdb=" N LYS E 375 " pdb=" CA LYS E 375 " pdb=" CB LYS E 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C LYS B 375 " pdb=" N LYS B 375 " pdb=" CA LYS B 375 " pdb=" CB LYS B 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C LYS F 375 " pdb=" N LYS F 375 " pdb=" CA LYS F 375 " pdb=" CB LYS F 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 25341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.936: 6360 0.936 - 1.873: 0 1.873 - 2.809: 0 2.809 - 3.745: 0 3.745 - 4.681: 8 Chirality restraints: 6368 Sorted by residual: chirality pdb=" C1B NAD B 801 " pdb=" C2B NAD B 801 " pdb=" N9A NAD B 801 " pdb=" O4B NAD B 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.48e+02 chirality pdb=" C1B NAD G 801 " pdb=" C2B NAD G 801 " pdb=" N9A NAD G 801 " pdb=" O4B NAD G 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.48e+02 chirality pdb=" C1B NAD F 801 " pdb=" C2B NAD F 801 " pdb=" N9A NAD F 801 " pdb=" O4B NAD F 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.47e+02 ... (remaining 6365 not shown) Planarity restraints: 7224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 801 " -0.248 2.00e-02 2.50e+03 1.57e-01 4.92e+02 pdb=" C2N NAD B 801 " 0.223 2.00e-02 2.50e+03 pdb=" C3N NAD B 801 " -0.007 2.00e-02 2.50e+03 pdb=" C4N NAD B 801 " -0.220 2.00e-02 2.50e+03 pdb=" C5N NAD B 801 " 0.015 2.00e-02 2.50e+03 pdb=" C6N NAD B 801 " 0.173 2.00e-02 2.50e+03 pdb=" C7N NAD B 801 " -0.017 2.00e-02 2.50e+03 pdb=" N1N NAD B 801 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 801 " 0.248 2.00e-02 2.50e+03 1.57e-01 4.92e+02 pdb=" C2N NAD F 801 " -0.223 2.00e-02 2.50e+03 pdb=" C3N NAD F 801 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAD F 801 " 0.220 2.00e-02 2.50e+03 pdb=" C5N NAD F 801 " -0.015 2.00e-02 2.50e+03 pdb=" C6N NAD F 801 " -0.173 2.00e-02 2.50e+03 pdb=" C7N NAD F 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1N NAD F 801 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 801 " 0.248 2.00e-02 2.50e+03 1.57e-01 4.91e+02 pdb=" C2N NAD C 801 " -0.223 2.00e-02 2.50e+03 pdb=" C3N NAD C 801 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD C 801 " 0.221 2.00e-02 2.50e+03 pdb=" C5N NAD C 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6N NAD C 801 " -0.172 2.00e-02 2.50e+03 pdb=" C7N NAD C 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1N NAD C 801 " -0.081 2.00e-02 2.50e+03 ... (remaining 7221 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9701 2.81 - 3.33: 40054 3.33 - 3.86: 69717 3.86 - 4.38: 91658 4.38 - 4.90: 138259 Nonbonded interactions: 349389 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" OG SER A 387 " model vdw 2.288 2.440 nonbonded pdb=" OG SER E 381 " pdb=" OG SER E 387 " model vdw 2.288 2.440 nonbonded pdb=" OG SER C 381 " pdb=" OG SER C 387 " model vdw 2.288 2.440 nonbonded pdb=" OG SER G 381 " pdb=" OG SER G 387 " model vdw 2.288 2.440 nonbonded pdb=" OG SER H 381 " pdb=" OG SER H 387 " model vdw 2.288 2.440 ... (remaining 349384 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.380 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: 10.890 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 100.470 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.290 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: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 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 : 0.010 0.215 41232 Z= 0.630 Angle : 1.981 16.703 55832 Z= 1.315 Chirality : 0.199 4.681 6368 Planarity : 0.009 0.157 7224 Dihedral : 19.395 98.908 15776 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.45 % Allowed : 14.67 % Favored : 78.88 % Cbeta Deviations : 1.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.08), residues: 5144 helix: -3.91 (0.05), residues: 3504 sheet: -3.30 (0.28), residues: 120 loop : -2.77 (0.13), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP D 420 HIS 0.019 0.004 HIS C 534 PHE 0.055 0.009 PHE D 466 TYR 0.041 0.009 TYR A 380 ARG 0.044 0.002 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 144 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 608 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 672 MET cc_start: 0.8400 (ptm) cc_final: 0.8057 (ptp) REVERT: B 590 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 590 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 608 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 672 MET cc_start: 0.8398 (ptm) cc_final: 0.8058 (ptp) REVERT: D 590 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (p) REVERT: E 590 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8624 (p) REVERT: E 608 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8837 (mp) REVERT: E 672 MET cc_start: 0.8382 (ptm) cc_final: 0.8035 (ptp) REVERT: F 590 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 590 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 608 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 672 MET cc_start: 0.8397 (ptm) cc_final: 0.8055 (ptp) REVERT: H 590 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8623 (p) outliers start: 276 outliers final: 48 residues processed: 420 average time/residue: 1.3934 time to fit residues: 711.5225 Evaluate side-chains 137 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 77 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 350 CYS Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 482 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 350 CYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 590 SER Chi-restraints excluded: chain E residue 608 ILE Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain F residue 590 SER Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 297 GLU Chi-restraints excluded: chain G residue 350 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 590 SER Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 350 CYS Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 590 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 432 optimal weight: 0.5980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 464 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 150 GLN A 232 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 516 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 642 GLN B 150 GLN B 232 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN C 97 GLN C 150 GLN C 232 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 516 HIS ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 642 GLN D 150 GLN D 232 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 HIS ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN E 97 GLN E 150 GLN E 232 ASN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 516 HIS ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 642 GLN F 150 GLN F 232 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 GLN F 516 HIS ** F 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 642 GLN G 97 GLN G 150 GLN G 232 ASN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 516 HIS ** G 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 642 GLN H 150 GLN H 232 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 GLN H 516 HIS ** H 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 642 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41232 Z= 0.213 Angle : 0.618 10.239 55832 Z= 0.318 Chirality : 0.038 0.163 6368 Planarity : 0.004 0.027 7224 Dihedral : 9.890 83.521 6128 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.43 % Allowed : 15.89 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.11), residues: 5144 helix: -1.44 (0.08), residues: 3512 sheet: -1.84 (0.35), residues: 120 loop : -1.42 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 420 HIS 0.004 0.001 HIS A 640 PHE 0.015 0.001 PHE E 308 TYR 0.011 0.001 TYR E 687 ARG 0.007 0.001 ARG F 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 113 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9700 (m-40) cc_final: 0.9471 (p0) REVERT: B 337 ASN cc_start: 0.9714 (m-40) cc_final: 0.9482 (p0) REVERT: B 672 MET cc_start: 0.8008 (ptt) cc_final: 0.7374 (ptt) REVERT: C 337 ASN cc_start: 0.9700 (m-40) cc_final: 0.9469 (p0) REVERT: D 337 ASN cc_start: 0.9714 (m-40) cc_final: 0.9483 (p0) REVERT: D 672 MET cc_start: 0.8007 (ptt) cc_final: 0.7374 (ptt) REVERT: E 337 ASN cc_start: 0.9701 (m-40) cc_final: 0.9470 (p0) REVERT: F 337 ASN cc_start: 0.9714 (m-40) cc_final: 0.9480 (p0) REVERT: F 672 MET cc_start: 0.8015 (ptt) cc_final: 0.7381 (ptt) REVERT: G 337 ASN cc_start: 0.9701 (m-40) cc_final: 0.9469 (p0) REVERT: H 337 ASN cc_start: 0.9713 (m-40) cc_final: 0.9482 (p0) REVERT: H 672 MET cc_start: 0.8009 (ptt) cc_final: 0.7377 (ptt) outliers start: 104 outliers final: 28 residues processed: 209 average time/residue: 1.5019 time to fit residues: 388.9511 Evaluate side-chains 125 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 607 LEU Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 258 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 386 optimal weight: 0.9980 chunk 316 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 465 optimal weight: 9.9990 chunk 503 optimal weight: 30.0000 chunk 414 optimal weight: 8.9990 chunk 461 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 373 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 642 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 616 ASN B 642 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 616 ASN C 642 GLN D 134 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 GLN D 616 ASN D 642 GLN E 134 GLN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 642 GLN F 134 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 616 ASN F 642 GLN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** G 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 642 GLN H 134 GLN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN H 616 ASN H 642 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9246 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 41232 Z= 0.480 Angle : 0.660 7.011 55832 Z= 0.339 Chirality : 0.041 0.165 6368 Planarity : 0.004 0.028 7224 Dihedral : 9.126 89.288 6064 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.82 % Allowed : 16.85 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 5144 helix: -0.56 (0.09), residues: 3528 sheet: -1.00 (0.37), residues: 120 loop : -0.78 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 420 HIS 0.004 0.001 HIS F 685 PHE 0.018 0.002 PHE A 308 TYR 0.010 0.002 TYR A 687 ARG 0.004 0.000 ARG E 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 85 time to evaluate : 4.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9729 (m-40) cc_final: 0.9510 (p0) REVERT: A 672 MET cc_start: 0.8220 (ptm) cc_final: 0.7804 (ptm) REVERT: B 337 ASN cc_start: 0.9735 (m-40) cc_final: 0.9497 (p0) REVERT: B 672 MET cc_start: 0.8216 (ptt) cc_final: 0.7594 (ptt) REVERT: C 337 ASN cc_start: 0.9728 (m-40) cc_final: 0.9510 (p0) REVERT: C 672 MET cc_start: 0.8218 (ptm) cc_final: 0.7803 (ptm) REVERT: D 337 ASN cc_start: 0.9735 (m-40) cc_final: 0.9498 (p0) REVERT: D 672 MET cc_start: 0.8212 (ptt) cc_final: 0.7594 (ptt) REVERT: E 337 ASN cc_start: 0.9729 (m-40) cc_final: 0.9510 (p0) REVERT: E 672 MET cc_start: 0.8217 (ptm) cc_final: 0.7801 (ptm) REVERT: F 337 ASN cc_start: 0.9735 (m-40) cc_final: 0.9498 (p0) REVERT: F 672 MET cc_start: 0.8210 (ptt) cc_final: 0.7591 (ptt) REVERT: G 337 ASN cc_start: 0.9729 (m-40) cc_final: 0.9509 (p0) REVERT: G 672 MET cc_start: 0.8220 (ptm) cc_final: 0.7803 (ptm) REVERT: H 337 ASN cc_start: 0.9734 (m-40) cc_final: 0.9498 (p0) REVERT: H 672 MET cc_start: 0.8164 (ptt) cc_final: 0.7534 (ptt) outliers start: 78 outliers final: 24 residues processed: 163 average time/residue: 1.5269 time to fit residues: 309.9447 Evaluate side-chains 104 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 460 optimal weight: 0.6980 chunk 350 optimal weight: 10.0000 chunk 241 optimal weight: 0.0970 chunk 51 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 467 optimal weight: 2.9990 chunk 494 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 443 optimal weight: 40.0000 chunk 133 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 631 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 631 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 631 GLN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN G 631 GLN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41232 Z= 0.169 Angle : 0.481 6.428 55832 Z= 0.247 Chirality : 0.036 0.140 6368 Planarity : 0.003 0.028 7224 Dihedral : 8.654 81.674 6052 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.29 % Allowed : 16.82 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 5144 helix: 0.30 (0.09), residues: 3544 sheet: -0.22 (0.39), residues: 120 loop : -0.34 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 420 HIS 0.004 0.001 HIS D 640 PHE 0.010 0.001 PHE G 308 TYR 0.004 0.001 TYR A 380 ARG 0.004 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 85 time to evaluate : 4.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9712 (m-40) cc_final: 0.9496 (p0) REVERT: A 672 MET cc_start: 0.8237 (ptm) cc_final: 0.7823 (ptm) REVERT: B 337 ASN cc_start: 0.9721 (m-40) cc_final: 0.9482 (p0) REVERT: B 672 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7473 (ptt) REVERT: C 337 ASN cc_start: 0.9711 (m-40) cc_final: 0.9495 (p0) REVERT: C 672 MET cc_start: 0.8236 (ptm) cc_final: 0.7822 (ptm) REVERT: D 337 ASN cc_start: 0.9721 (m-40) cc_final: 0.9482 (p0) REVERT: D 672 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7473 (ptt) REVERT: E 337 ASN cc_start: 0.9712 (m-40) cc_final: 0.9496 (p0) REVERT: E 672 MET cc_start: 0.8232 (ptm) cc_final: 0.7819 (ptm) REVERT: F 337 ASN cc_start: 0.9721 (m-40) cc_final: 0.9481 (p0) REVERT: F 672 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7475 (ptt) REVERT: G 337 ASN cc_start: 0.9712 (m-40) cc_final: 0.9495 (p0) REVERT: G 672 MET cc_start: 0.8235 (ptm) cc_final: 0.7821 (ptm) REVERT: H 337 ASN cc_start: 0.9720 (m-40) cc_final: 0.9481 (p0) REVERT: H 672 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7511 (ptt) outliers start: 55 outliers final: 16 residues processed: 136 average time/residue: 1.4348 time to fit residues: 248.7496 Evaluate side-chains 100 residues out of total 4280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 672 MET Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 127 ASP Chi-restraints excluded: chain H residue 667 VAL Chi-restraints excluded: chain H residue 672 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 412 optimal weight: 0.0470 chunk 280 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 422 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 252 optimal weight: 9.9990 chunk 444 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 overall best weight: 3.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 239 GLN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 239 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN F 239 GLN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 GLN ** F 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** G 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 GLN ** H 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.3090 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: