Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 05:39:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9s_12105/10_2023/7b9s_12105.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 378 5.16 5 C 46572 2.51 5 N 12600 2.21 5 O 12480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 108": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "X ARG 70": "NH1" <-> "NH2" Residue "X GLU 93": "OE1" <-> "OE2" Residue "X ARG 322": "NH1" <-> "NH2" Residue "X GLU 478": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ARG 208": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H ARG 242": "NH1" <-> "NH2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I ARG 322": "NH1" <-> "NH2" Residue "I GLU 478": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ARG 208": "NH1" <-> "NH2" Residue "M ARG 238": "NH1" <-> "NH2" Residue "M ARG 242": "NH1" <-> "NH2" Residue "M GLU 248": "OE1" <-> "OE2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "N ARG 322": "NH1" <-> "NH2" Residue "N GLU 478": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 120": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "L ARG 129": "NH1" <-> "NH2" Residue "L TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 320": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "R GLU 144": "OE1" <-> "OE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R ARG 242": "NH1" <-> "NH2" Residue "R GLU 248": "OE1" <-> "OE2" Residue "S ASP 47": "OD1" <-> "OD2" Residue "S ARG 70": "NH1" <-> "NH2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S ARG 322": "NH1" <-> "NH2" Residue "S GLU 340": "OE1" <-> "OE2" Residue "S GLU 478": "OE1" <-> "OE2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 120": "OE1" <-> "OE2" Residue "P GLU 150": "OE1" <-> "OE2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 296": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q ARG 129": "NH1" <-> "NH2" Residue "Q TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 320": "OE1" <-> "OE2" Residue "Q ARG 322": "NH1" <-> "NH2" Residue "Q GLU 497": "OE1" <-> "OE2" Residue "O ARG 39": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "Y ARG 108": "NH1" <-> "NH2" Residue "Y GLU 144": "OE1" <-> "OE2" Residue "Y ARG 208": "NH1" <-> "NH2" Residue "Y ARG 238": "NH1" <-> "NH2" Residue "Y ARG 242": "NH1" <-> "NH2" Residue "Y GLU 248": "OE1" <-> "OE2" Residue "Z ARG 70": "NH1" <-> "NH2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z ARG 322": "NH1" <-> "NH2" Residue "Z GLU 478": "OE1" <-> "OE2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "V GLU 120": "OE1" <-> "OE2" Residue "V GLU 150": "OE1" <-> "OE2" Residue "V GLU 173": "OE1" <-> "OE2" Residue "V TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 296": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ARG 129": "NH1" <-> "NH2" Residue "W TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 320": "OE1" <-> "OE2" Residue "W GLU 475": "OE1" <-> "OE2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 41": "NH1" <-> "NH2" Residue "T ARG 51": "NH1" <-> "NH2" Residue "4 ARG 108": "NH1" <-> "NH2" Residue "4 GLU 144": "OE1" <-> "OE2" Residue "4 ARG 208": "NH1" <-> "NH2" Residue "4 ARG 238": "NH1" <-> "NH2" Residue "4 ARG 242": "NH1" <-> "NH2" Residue "4 GLU 248": "OE1" <-> "OE2" Residue "5 ARG 70": "NH1" <-> "NH2" Residue "5 GLU 93": "OE1" <-> "OE2" Residue "5 ARG 322": "NH1" <-> "NH2" Residue "5 GLU 478": "OE1" <-> "OE2" Residue "2 GLU 33": "OE1" <-> "OE2" Residue "2 GLU 116": "OE1" <-> "OE2" Residue "2 GLU 120": "OE1" <-> "OE2" Residue "2 GLU 150": "OE1" <-> "OE2" Residue "2 GLU 173": "OE1" <-> "OE2" Residue "2 TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 296": "OE1" <-> "OE2" Residue "3 ARG 129": "NH1" <-> "NH2" Residue "3 TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 72030 Number of models: 1 Model: "" Number of chains: 30 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "X" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "H" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "I" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "F" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "G" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "M" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "N" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "K" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "L" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "R" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "S" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "P" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "Q" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "O" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "Y" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "Z" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "V" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "W" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "T" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1305 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain breaks: 3 Chain: "5" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3469 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "2" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3107 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 29, 'TRANS': 366} Chain breaks: 1 Chain: "3" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3644 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain: "1" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 480 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Time building chain proxies: 27.00, per 1000 atoms: 0.37 Number of scatterers: 72030 At special positions: 0 Unit cell: (267.03, 287.67, 125.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 378 16.00 O 12480 8.00 N 12600 7.00 C 46572 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: 23.16 Conformation dependent library (CDL) restraints added in 7.7 seconds 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17460 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 53 sheets defined 59.9% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'E' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA E 147 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'X' and resid 41 through 60 removed outlier: 3.578A pdb=" N MET X 45 " --> pdb=" O PRO X 41 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP X 47 " --> pdb=" O SER X 43 " (cutoff:3.500A) Proline residue: X 48 - end of helix Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 134 through 164 removed outlier: 3.678A pdb=" N GLN X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 191 removed outlier: 3.866A pdb=" N PHE X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 196 No H-bonds generated for 'chain 'X' and resid 194 through 196' Processing helix chain 'X' and resid 197 through 218 removed outlier: 4.320A pdb=" N VAL X 209 " --> pdb=" O LEU X 205 " (cutoff:3.500A) Proline residue: X 210 - end of helix removed outlier: 3.520A pdb=" N THR X 218 " --> pdb=" O ALA X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 246 removed outlier: 3.859A pdb=" N MET X 243 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG X 244 " --> pdb=" O MET X 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 272 removed outlier: 4.082A pdb=" N TYR X 253 " --> pdb=" O ARG X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 276 through 303 Proline residue: X 296 - end of helix Processing helix chain 'X' and resid 312 through 320 Processing helix chain 'X' and resid 340 through 378 removed outlier: 4.011A pdb=" N SER X 344 " --> pdb=" O GLU X 340 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU X 389 " --> pdb=" O ARG X 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU X 390 " --> pdb=" O TRP X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE X 423 " --> pdb=" O ALA X 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL X 433 " --> pdb=" O ARG X 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 460 Proline residue: X 451 - end of helix removed outlier: 4.406A pdb=" N ALA X 458 " --> pdb=" O GLY X 454 " (cutoff:3.500A) Processing helix chain 'X' and resid 461 through 465 Processing helix chain 'X' and resid 467 through 481 Processing helix chain 'X' and resid 484 through 494 Processing helix chain 'C' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL C 40 " --> pdb=" O PRO C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.912A pdb=" N ALA C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 96 through 133 Processing helix chain 'C' and resid 135 through 142 removed outlier: 3.665A pdb=" N ALA C 140 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 226 through 245 Processing helix chain 'C' and resid 258 through 270 removed outlier: 3.522A pdb=" N ASP C 263 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP C 264 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 266 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP C 267 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 401 through 413 Processing helix chain 'D' and resid 41 through 60 removed outlier: 4.255A pdb=" N ASP D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Proline residue: D 48 - end of helix removed outlier: 4.358A pdb=" N LYS D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.974A pdb=" N SER D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 164 removed outlier: 3.654A pdb=" N GLN D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Proline residue: D 210 - end of helix removed outlier: 3.851A pdb=" N ALA D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 246 removed outlier: 3.849A pdb=" N PHE D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 274 Processing helix chain 'D' and resid 276 through 303 removed outlier: 3.850A pdb=" N HIS D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 346 through 374 removed outlier: 4.051A pdb=" N LEU D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 403 removed outlier: 3.764A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 408 through 434 removed outlier: 3.680A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 467 through 483 removed outlier: 3.761A pdb=" N GLU D 478 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 494 through 500 Processing helix chain 'B' and resid 19 through 39 Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA H 147 " --> pdb=" O GLU H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'H' and resid 209 through 214 Processing helix chain 'H' and resid 218 through 235 Processing helix chain 'H' and resid 245 through 258 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'I' and resid 41 through 60 removed outlier: 3.788A pdb=" N MET I 45 " --> pdb=" O PRO I 41 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASP I 47 " --> pdb=" O SER I 43 " (cutoff:3.500A) Proline residue: I 48 - end of helix Processing helix chain 'I' and resid 117 through 130 removed outlier: 3.593A pdb=" N LYS I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 164 removed outlier: 3.690A pdb=" N GLN I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 191 removed outlier: 3.865A pdb=" N PHE I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 197 through 218 removed outlier: 4.322A pdb=" N VAL I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) Proline residue: I 210 - end of helix removed outlier: 3.523A pdb=" N THR I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 246 removed outlier: 3.855A pdb=" N MET I 243 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG I 244 " --> pdb=" O MET I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 272 removed outlier: 4.077A pdb=" N TYR I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 303 Proline residue: I 296 - end of helix Processing helix chain 'I' and resid 312 through 320 Processing helix chain 'I' and resid 340 through 378 removed outlier: 3.784A pdb=" N SER I 344 " --> pdb=" O GLU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU I 389 " --> pdb=" O ARG I 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 390 " --> pdb=" O TRP I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 433 " --> pdb=" O ARG I 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 460 Proline residue: I 451 - end of helix removed outlier: 4.410A pdb=" N ALA I 458 " --> pdb=" O GLY I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 465 Processing helix chain 'I' and resid 467 through 481 Processing helix chain 'I' and resid 484 through 494 Processing helix chain 'F' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 83 removed outlier: 5.084A pdb=" N ALA F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 96 through 133 Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.665A pdb=" N ALA F 140 " --> pdb=" O THR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 226 through 245 Processing helix chain 'F' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP F 263 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP F 264 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS F 266 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP F 267 " --> pdb=" O TRP F 264 " (cutoff:3.500A) Proline residue: F 269 - end of helix Processing helix chain 'F' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL F 337 " --> pdb=" O GLN F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 401 through 413 Processing helix chain 'G' and resid 41 through 60 removed outlier: 4.259A pdb=" N ASP G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Proline residue: G 48 - end of helix removed outlier: 4.357A pdb=" N LYS G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 3.912A pdb=" N SER G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 164 removed outlier: 3.656A pdb=" N GLN G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 219 removed outlier: 4.662A pdb=" N GLY G 200 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL G 209 " --> pdb=" O LEU G 205 " (cutoff:3.500A) Proline residue: G 210 - end of helix removed outlier: 3.850A pdb=" N ALA G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 246 removed outlier: 3.844A pdb=" N PHE G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 274 Processing helix chain 'G' and resid 276 through 303 removed outlier: 3.911A pdb=" N HIS G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) Proline residue: G 296 - end of helix Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 346 through 374 removed outlier: 4.061A pdb=" N LEU G 350 " --> pdb=" O ARG G 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 403 removed outlier: 3.696A pdb=" N LEU G 389 " --> pdb=" O ARG G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 406 No H-bonds generated for 'chain 'G' and resid 404 through 406' Processing helix chain 'G' and resid 408 through 434 removed outlier: 3.679A pdb=" N ILE G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 461 Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 467 through 483 removed outlier: 3.691A pdb=" N GLU G 478 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR G 479 " --> pdb=" O GLU G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 494 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 removed outlier: 4.045A pdb=" N ALA M 147 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 208 Processing helix chain 'M' and resid 209 through 214 Processing helix chain 'M' and resid 218 through 235 Processing helix chain 'M' and resid 245 through 258 Processing helix chain 'M' and resid 298 through 303 Processing helix chain 'N' and resid 41 through 60 removed outlier: 3.684A pdb=" N MET N 45 " --> pdb=" O PRO N 41 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP N 47 " --> pdb=" O SER N 43 " (cutoff:3.500A) Proline residue: N 48 - end of helix Processing helix chain 'N' and resid 117 through 130 Processing helix chain 'N' and resid 134 through 164 removed outlier: 3.674A pdb=" N GLN N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 191 removed outlier: 3.861A pdb=" N PHE N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 196 No H-bonds generated for 'chain 'N' and resid 194 through 196' Processing helix chain 'N' and resid 197 through 218 removed outlier: 4.316A pdb=" N VAL N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) Proline residue: N 210 - end of helix removed outlier: 3.519A pdb=" N THR N 218 " --> pdb=" O ALA N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 246 removed outlier: 3.854A pdb=" N MET N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 272 removed outlier: 4.074A pdb=" N TYR N 253 " --> pdb=" O ARG N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 303 Proline residue: N 296 - end of helix Processing helix chain 'N' and resid 312 through 320 Processing helix chain 'N' and resid 340 through 378 removed outlier: 3.941A pdb=" N SER N 344 " --> pdb=" O GLU N 340 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL N 345 " --> pdb=" O GLY N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU N 389 " --> pdb=" O ARG N 385 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU N 390 " --> pdb=" O TRP N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 434 removed outlier: 3.737A pdb=" N ILE N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL N 433 " --> pdb=" O ARG N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 460 Proline residue: N 451 - end of helix removed outlier: 4.398A pdb=" N ALA N 458 " --> pdb=" O GLY N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 465 Processing helix chain 'N' and resid 467 through 481 Processing helix chain 'N' and resid 484 through 494 Processing helix chain 'K' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 90 Processing helix chain 'K' and resid 96 through 133 Processing helix chain 'K' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA K 140 " --> pdb=" O THR K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 203 Processing helix chain 'K' and resid 226 through 245 Processing helix chain 'K' and resid 258 through 270 removed outlier: 3.520A pdb=" N ASP K 263 " --> pdb=" O ASP K 260 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP K 264 " --> pdb=" O ARG K 261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 266 " --> pdb=" O ASP K 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP K 267 " --> pdb=" O TRP K 264 " (cutoff:3.500A) Proline residue: K 269 - end of helix Processing helix chain 'K' and resid 333 through 338 removed outlier: 4.009A pdb=" N VAL K 337 " --> pdb=" O GLN K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 401 through 413 Processing helix chain 'L' and resid 41 through 60 removed outlier: 4.267A pdb=" N ASP L 47 " --> pdb=" O SER L 43 " (cutoff:3.500A) Proline residue: L 48 - end of helix removed outlier: 4.386A pdb=" N LYS L 51 " --> pdb=" O ASP L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 127 removed outlier: 3.904A pdb=" N SER L 127 " --> pdb=" O ALA L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 164 removed outlier: 3.650A pdb=" N GLN L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 189 removed outlier: 4.287A pdb=" N PHE L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY L 200 " --> pdb=" O ASP L 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL L 209 " --> pdb=" O LEU L 205 " (cutoff:3.500A) Proline residue: L 210 - end of helix removed outlier: 3.849A pdb=" N ALA L 219 " --> pdb=" O ILE L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 246 removed outlier: 3.845A pdb=" N PHE L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 274 Processing helix chain 'L' and resid 276 through 303 removed outlier: 3.848A pdb=" N HIS L 293 " --> pdb=" O VAL L 289 " (cutoff:3.500A) Proline residue: L 296 - end of helix Processing helix chain 'L' and resid 343 through 346 Processing helix chain 'L' and resid 347 through 374 removed outlier: 3.809A pdb=" N GLU L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 403 removed outlier: 3.691A pdb=" N LEU L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 406 No H-bonds generated for 'chain 'L' and resid 404 through 406' Processing helix chain 'L' and resid 408 through 434 removed outlier: 3.642A pdb=" N ILE L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 461 Proline residue: L 451 - end of helix Processing helix chain 'L' and resid 467 through 483 removed outlier: 4.427A pdb=" N GLU L 478 " --> pdb=" O VAL L 474 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR L 479 " --> pdb=" O GLU L 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 494 Processing helix chain 'L' and resid 494 through 502 Processing helix chain 'J' and resid 19 through 39 Processing helix chain 'J' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA R 147 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 208 Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 218 through 235 Processing helix chain 'R' and resid 245 through 258 Processing helix chain 'R' and resid 298 through 303 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.779A pdb=" N MET S 45 " --> pdb=" O PRO S 41 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP S 47 " --> pdb=" O SER S 43 " (cutoff:3.500A) Proline residue: S 48 - end of helix Processing helix chain 'S' and resid 117 through 130 Processing helix chain 'S' and resid 134 through 164 removed outlier: 3.677A pdb=" N GLN S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 191 removed outlier: 3.866A pdb=" N PHE S 172 " --> pdb=" O LEU S 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 196 No H-bonds generated for 'chain 'S' and resid 194 through 196' Processing helix chain 'S' and resid 197 through 218 removed outlier: 4.320A pdb=" N VAL S 209 " --> pdb=" O LEU S 205 " (cutoff:3.500A) Proline residue: S 210 - end of helix removed outlier: 3.520A pdb=" N THR S 218 " --> pdb=" O ALA S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 224 through 246 removed outlier: 3.858A pdb=" N MET S 243 " --> pdb=" O ALA S 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG S 244 " --> pdb=" O MET S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 272 removed outlier: 4.080A pdb=" N TYR S 253 " --> pdb=" O ARG S 249 " (cutoff:3.500A) Processing helix chain 'S' and resid 276 through 303 Proline residue: S 296 - end of helix Processing helix chain 'S' and resid 312 through 320 Processing helix chain 'S' and resid 341 through 378 removed outlier: 3.665A pdb=" N VAL S 345 " --> pdb=" O GLY S 341 " (cutoff:3.500A) Processing helix chain 'S' and resid 385 through 406 removed outlier: 3.912A pdb=" N LEU S 389 " --> pdb=" O ARG S 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 390 " --> pdb=" O TRP S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 434 removed outlier: 3.733A pdb=" N ILE S 423 " --> pdb=" O ALA S 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL S 433 " --> pdb=" O ARG S 429 " (cutoff:3.500A) Processing helix chain 'S' and resid 436 through 460 Proline residue: S 451 - end of helix removed outlier: 4.405A pdb=" N ALA S 458 " --> pdb=" O GLY S 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 461 through 465 Processing helix chain 'S' and resid 467 through 481 Processing helix chain 'S' and resid 484 through 494 Processing helix chain 'P' and resid 36 through 61 removed outlier: 3.860A pdb=" N VAL P 40 " --> pdb=" O PRO P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA P 70 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 83 removed outlier: 5.086A pdb=" N ALA P 81 " --> pdb=" O ILE P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 90 Processing helix chain 'P' and resid 96 through 133 Processing helix chain 'P' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA P 140 " --> pdb=" O THR P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY P 161 " --> pdb=" O ASP P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 203 Processing helix chain 'P' and resid 226 through 245 Processing helix chain 'P' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP P 263 " --> pdb=" O ASP P 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP P 264 " --> pdb=" O ARG P 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS P 266 " --> pdb=" O ASP P 263 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP P 267 " --> pdb=" O TRP P 264 " (cutoff:3.500A) Proline residue: P 269 - end of helix Processing helix chain 'P' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL P 337 " --> pdb=" O GLN P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 360 through 362 No H-bonds generated for 'chain 'P' and resid 360 through 362' Processing helix chain 'P' and resid 401 through 413 Processing helix chain 'Q' and resid 41 through 60 removed outlier: 4.255A pdb=" N ASP Q 47 " --> pdb=" O SER Q 43 " (cutoff:3.500A) Proline residue: Q 48 - end of helix removed outlier: 4.358A pdb=" N LYS Q 51 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 127 removed outlier: 4.053A pdb=" N SER Q 127 " --> pdb=" O ALA Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 164 removed outlier: 3.654A pdb=" N GLN Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 189 removed outlier: 4.288A pdb=" N PHE Q 172 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY Q 200 " --> pdb=" O ASP Q 196 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL Q 209 " --> pdb=" O LEU Q 205 " (cutoff:3.500A) Proline residue: Q 210 - end of helix removed outlier: 3.851A pdb=" N ALA Q 219 " --> pdb=" O ILE Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 246 removed outlier: 3.849A pdb=" N PHE Q 232 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 274 Processing helix chain 'Q' and resid 276 through 303 removed outlier: 3.853A pdb=" N HIS Q 293 " --> pdb=" O VAL Q 289 " (cutoff:3.500A) Proline residue: Q 296 - end of helix Processing helix chain 'Q' and resid 343 through 345 No H-bonds generated for 'chain 'Q' and resid 343 through 345' Processing helix chain 'Q' and resid 346 through 374 removed outlier: 4.032A pdb=" N LEU Q 350 " --> pdb=" O ARG Q 346 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU Q 353 " --> pdb=" O LEU Q 349 " (cutoff:3.500A) Processing helix chain 'Q' and resid 385 through 403 removed outlier: 3.688A pdb=" N LEU Q 389 " --> pdb=" O ARG Q 385 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 434 removed outlier: 3.677A pdb=" N ILE Q 423 " --> pdb=" O ALA Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 436 through 461 Proline residue: Q 451 - end of helix Processing helix chain 'Q' and resid 467 through 483 removed outlier: 3.728A pdb=" N GLU Q 478 " --> pdb=" O VAL Q 474 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR Q 479 " --> pdb=" O GLU Q 475 " (cutoff:3.500A) Processing helix chain 'Q' and resid 484 through 494 Processing helix chain 'Q' and resid 494 through 501 removed outlier: 3.701A pdb=" N TYR Q 501 " --> pdb=" O GLU Q 497 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 39 Processing helix chain 'O' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA Y 147 " --> pdb=" O GLU Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 208 Processing helix chain 'Y' and resid 209 through 214 Processing helix chain 'Y' and resid 218 through 235 Processing helix chain 'Y' and resid 245 through 258 Processing helix chain 'Y' and resid 298 through 303 Processing helix chain 'Z' and resid 41 through 60 removed outlier: 3.665A pdb=" N MET Z 45 " --> pdb=" O PRO Z 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP Z 47 " --> pdb=" O SER Z 43 " (cutoff:3.500A) Proline residue: Z 48 - end of helix Processing helix chain 'Z' and resid 117 through 130 removed outlier: 3.695A pdb=" N LYS Z 128 " --> pdb=" O THR Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 164 removed outlier: 3.684A pdb=" N GLN Z 140 " --> pdb=" O VAL Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 191 removed outlier: 3.863A pdb=" N PHE Z 172 " --> pdb=" O LEU Z 168 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 196 No H-bonds generated for 'chain 'Z' and resid 194 through 196' Processing helix chain 'Z' and resid 197 through 218 removed outlier: 4.323A pdb=" N VAL Z 209 " --> pdb=" O LEU Z 205 " (cutoff:3.500A) Proline residue: Z 210 - end of helix removed outlier: 3.522A pdb=" N THR Z 218 " --> pdb=" O ALA Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 246 removed outlier: 3.856A pdb=" N MET Z 243 " --> pdb=" O ALA Z 239 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG Z 244 " --> pdb=" O MET Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 249 through 272 removed outlier: 4.078A pdb=" N TYR Z 253 " --> pdb=" O ARG Z 249 " (cutoff:3.500A) Processing helix chain 'Z' and resid 276 through 303 Proline residue: Z 296 - end of helix Processing helix chain 'Z' and resid 312 through 320 Processing helix chain 'Z' and resid 340 through 378 removed outlier: 3.808A pdb=" N SER Z 344 " --> pdb=" O GLU Z 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Z 345 " --> pdb=" O GLY Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU Z 389 " --> pdb=" O ARG Z 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Z 390 " --> pdb=" O TRP Z 386 " (cutoff:3.500A) Processing helix chain 'Z' and resid 408 through 434 removed outlier: 3.734A pdb=" N ILE Z 423 " --> pdb=" O ALA Z 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL Z 433 " --> pdb=" O ARG Z 429 " (cutoff:3.500A) Processing helix chain 'Z' and resid 436 through 460 Proline residue: Z 451 - end of helix removed outlier: 4.409A pdb=" N ALA Z 458 " --> pdb=" O GLY Z 454 " (cutoff:3.500A) Processing helix chain 'Z' and resid 461 through 465 Processing helix chain 'Z' and resid 467 through 481 Processing helix chain 'Z' and resid 484 through 494 Processing helix chain 'V' and resid 36 through 61 removed outlier: 3.861A pdb=" N VAL V 40 " --> pdb=" O PRO V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 72 removed outlier: 3.912A pdb=" N ALA V 70 " --> pdb=" O LEU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 83 removed outlier: 5.084A pdb=" N ALA V 81 " --> pdb=" O ILE V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 90 Processing helix chain 'V' and resid 96 through 133 Processing helix chain 'V' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA V 140 " --> pdb=" O THR V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 161 removed outlier: 4.385A pdb=" N GLY V 161 " --> pdb=" O ASP V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 189 through 203 Processing helix chain 'V' and resid 226 through 245 Processing helix chain 'V' and resid 258 through 270 removed outlier: 3.522A pdb=" N ASP V 263 " --> pdb=" O ASP V 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP V 264 " --> pdb=" O ARG V 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS V 266 " --> pdb=" O ASP V 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP V 267 " --> pdb=" O TRP V 264 " (cutoff:3.500A) Proline residue: V 269 - end of helix Processing helix chain 'V' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL V 337 " --> pdb=" O GLN V 333 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 362 No H-bonds generated for 'chain 'V' and resid 360 through 362' Processing helix chain 'V' and resid 401 through 413 Processing helix chain 'W' and resid 41 through 60 removed outlier: 4.260A pdb=" N ASP W 47 " --> pdb=" O SER W 43 " (cutoff:3.500A) Proline residue: W 48 - end of helix removed outlier: 4.357A pdb=" N LYS W 51 " --> pdb=" O ASP W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 127 removed outlier: 4.147A pdb=" N SER W 127 " --> pdb=" O ALA W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 134 through 164 removed outlier: 3.657A pdb=" N GLN W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 189 removed outlier: 4.286A pdb=" N PHE W 172 " --> pdb=" O LEU W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 219 removed outlier: 4.661A pdb=" N GLY W 200 " --> pdb=" O ASP W 196 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL W 209 " --> pdb=" O LEU W 205 " (cutoff:3.500A) Proline residue: W 210 - end of helix removed outlier: 3.851A pdb=" N ALA W 219 " --> pdb=" O ILE W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 246 removed outlier: 3.846A pdb=" N PHE W 232 " --> pdb=" O ALA W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 249 through 274 Processing helix chain 'W' and resid 276 through 303 removed outlier: 3.871A pdb=" N HIS W 293 " --> pdb=" O VAL W 289 " (cutoff:3.500A) Proline residue: W 296 - end of helix Processing helix chain 'W' and resid 343 through 346 Processing helix chain 'W' and resid 347 through 374 removed outlier: 3.769A pdb=" N GLU W 353 " --> pdb=" O LEU W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 403 removed outlier: 3.691A pdb=" N LEU W 389 " --> pdb=" O ARG W 385 " (cutoff:3.500A) Processing helix chain 'W' and resid 404 through 406 No H-bonds generated for 'chain 'W' and resid 404 through 406' Processing helix chain 'W' and resid 408 through 434 removed outlier: 3.670A pdb=" N ILE W 423 " --> pdb=" O ALA W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 436 through 461 Proline residue: W 451 - end of helix Processing helix chain 'W' and resid 467 through 483 removed outlier: 3.950A pdb=" N GLU W 478 " --> pdb=" O VAL W 474 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR W 479 " --> pdb=" O GLU W 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 484 through 494 Processing helix chain 'W' and resid 494 through 502 Processing helix chain 'T' and resid 19 through 39 Processing helix chain 'T' and resid 47 through 72 removed outlier: 3.711A pdb=" N ARG T 51 " --> pdb=" O GLU T 47 " (cutoff:3.500A) Processing helix chain '4' and resid 144 through 151 removed outlier: 4.044A pdb=" N ALA 4 147 " --> pdb=" O GLU 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 205 through 208 Processing helix chain '4' and resid 209 through 214 Processing helix chain '4' and resid 218 through 235 Processing helix chain '4' and resid 245 through 258 Processing helix chain '4' and resid 298 through 303 Processing helix chain '5' and resid 41 through 60 removed outlier: 3.588A pdb=" N MET 5 45 " --> pdb=" O PRO 5 41 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Proline residue: 5 48 - end of helix Processing helix chain '5' and resid 117 through 130 Processing helix chain '5' and resid 134 through 164 removed outlier: 3.676A pdb=" N GLN 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 168 through 191 removed outlier: 3.861A pdb=" N PHE 5 172 " --> pdb=" O LEU 5 168 " (cutoff:3.500A) Processing helix chain '5' and resid 194 through 196 No H-bonds generated for 'chain '5' and resid 194 through 196' Processing helix chain '5' and resid 197 through 218 removed outlier: 4.316A pdb=" N VAL 5 209 " --> pdb=" O LEU 5 205 " (cutoff:3.500A) Proline residue: 5 210 - end of helix removed outlier: 3.517A pdb=" N THR 5 218 " --> pdb=" O ALA 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 224 through 246 removed outlier: 3.854A pdb=" N MET 5 243 " --> pdb=" O ALA 5 239 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG 5 244 " --> pdb=" O MET 5 240 " (cutoff:3.500A) Processing helix chain '5' and resid 249 through 272 removed outlier: 4.077A pdb=" N TYR 5 253 " --> pdb=" O ARG 5 249 " (cutoff:3.500A) Processing helix chain '5' and resid 276 through 303 Proline residue: 5 296 - end of helix Processing helix chain '5' and resid 312 through 320 Processing helix chain '5' and resid 341 through 378 removed outlier: 3.503A pdb=" N VAL 5 345 " --> pdb=" O GLY 5 341 " (cutoff:3.500A) Processing helix chain '5' and resid 385 through 406 removed outlier: 3.913A pdb=" N LEU 5 389 " --> pdb=" O ARG 5 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 5 390 " --> pdb=" O TRP 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 408 through 434 removed outlier: 3.738A pdb=" N ILE 5 423 " --> pdb=" O ALA 5 419 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL 5 433 " --> pdb=" O ARG 5 429 " (cutoff:3.500A) Processing helix chain '5' and resid 436 through 460 Proline residue: 5 451 - end of helix removed outlier: 4.401A pdb=" N ALA 5 458 " --> pdb=" O GLY 5 454 " (cutoff:3.500A) Processing helix chain '5' and resid 461 through 465 Processing helix chain '5' and resid 467 through 481 Processing helix chain '5' and resid 484 through 494 Processing helix chain '2' and resid 36 through 61 removed outlier: 3.860A pdb=" N VAL 2 40 " --> pdb=" O PRO 2 36 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 72 removed outlier: 3.913A pdb=" N ALA 2 70 " --> pdb=" O LEU 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 75 through 83 removed outlier: 5.085A pdb=" N ALA 2 81 " --> pdb=" O ILE 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 90 Processing helix chain '2' and resid 96 through 133 Processing helix chain '2' and resid 135 through 142 removed outlier: 3.664A pdb=" N ALA 2 140 " --> pdb=" O THR 2 137 " (cutoff:3.500A) Processing helix chain '2' and resid 156 through 161 removed outlier: 4.386A pdb=" N GLY 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 203 Processing helix chain '2' and resid 226 through 245 Processing helix chain '2' and resid 258 through 270 removed outlier: 3.521A pdb=" N ASP 2 263 " --> pdb=" O ASP 2 260 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TRP 2 264 " --> pdb=" O ARG 2 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS 2 266 " --> pdb=" O ASP 2 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP 2 267 " --> pdb=" O TRP 2 264 " (cutoff:3.500A) Proline residue: 2 269 - end of helix Processing helix chain '2' and resid 333 through 338 removed outlier: 4.008A pdb=" N VAL 2 337 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) Processing helix chain '2' and resid 360 through 362 No H-bonds generated for 'chain '2' and resid 360 through 362' Processing helix chain '2' and resid 401 through 413 Processing helix chain '3' and resid 41 through 60 removed outlier: 3.501A pdb=" N MET 3 45 " --> pdb=" O PRO 3 41 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP 3 47 " --> pdb=" O SER 3 43 " (cutoff:3.500A) Proline residue: 3 48 - end of helix removed outlier: 4.359A pdb=" N LYS 3 51 " --> pdb=" O ASP 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 127 removed outlier: 3.949A pdb=" N SER 3 127 " --> pdb=" O ALA 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 134 through 164 removed outlier: 3.651A pdb=" N GLN 3 140 " --> pdb=" O VAL 3 136 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 189 removed outlier: 4.287A pdb=" N PHE 3 172 " --> pdb=" O LEU 3 168 " (cutoff:3.500A) Processing helix chain '3' and resid 196 through 219 removed outlier: 4.660A pdb=" N GLY 3 200 " --> pdb=" O ASP 3 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL 3 209 " --> pdb=" O LEU 3 205 " (cutoff:3.500A) Proline residue: 3 210 - end of helix removed outlier: 3.851A pdb=" N ALA 3 219 " --> pdb=" O ILE 3 215 " (cutoff:3.500A) Processing helix chain '3' and resid 228 through 246 removed outlier: 3.844A pdb=" N PHE 3 232 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) Processing helix chain '3' and resid 249 through 274 Processing helix chain '3' and resid 276 through 303 removed outlier: 3.818A pdb=" N HIS 3 293 " --> pdb=" O VAL 3 289 " (cutoff:3.500A) Proline residue: 3 296 - end of helix Processing helix chain '3' and resid 343 through 345 No H-bonds generated for 'chain '3' and resid 343 through 345' Processing helix chain '3' and resid 346 through 374 removed outlier: 4.076A pdb=" N LEU 3 350 " --> pdb=" O ARG 3 346 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU 3 353 " --> pdb=" O LEU 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 385 through 403 removed outlier: 3.687A pdb=" N LEU 3 389 " --> pdb=" O ARG 3 385 " (cutoff:3.500A) Processing helix chain '3' and resid 404 through 406 No H-bonds generated for 'chain '3' and resid 404 through 406' Processing helix chain '3' and resid 408 through 434 removed outlier: 3.692A pdb=" N ILE 3 423 " --> pdb=" O ALA 3 419 " (cutoff:3.500A) Processing helix chain '3' and resid 436 through 461 Proline residue: 3 451 - end of helix Processing helix chain '3' and resid 467 through 483 removed outlier: 4.139A pdb=" N GLU 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR 3 479 " --> pdb=" O GLU 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 484 through 494 Processing helix chain '3' and resid 494 through 502 Processing helix chain '1' and resid 19 through 39 Processing helix chain '1' and resid 47 through 72 removed outlier: 3.712A pdb=" N ARG 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.541A pdb=" N ARG E 242 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR E 198 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 71 through 77 removed outlier: 3.567A pdb=" N LEU X 100 " --> pdb=" O ALA X 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 214 removed outlier: 6.840A pdb=" N TYR C 207 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET C 169 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 209 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL C 167 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS C 211 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET C 169 " --> pdb=" O PHE C 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE C 394 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE C 393 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR C 376 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 373 " --> pdb=" O THR C 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU C 365 " --> pdb=" O TRP C 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 222 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 367 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL C 224 " --> pdb=" O PHE C 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP C 369 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR C 221 " --> pdb=" O ASP C 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS C 323 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE C 349 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 325 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR C 287 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 254 " --> pdb=" O TYR C 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 277 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 37 Processing sheet with id=AA9, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG H 242 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR H 198 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 71 through 77 removed outlier: 8.684A pdb=" N LEU I 100 " --> pdb=" O VAL I 22 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA I 24 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU I 102 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET I 26 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE I 104 " --> pdb=" O MET I 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AB6, first strand: chain 'F' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR F 207 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET F 169 " --> pdb=" O TYR F 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 209 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL F 167 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS F 211 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET F 169 " --> pdb=" O PHE F 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE F 394 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE F 393 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR F 376 " --> pdb=" O PHE F 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 373 " --> pdb=" O THR F 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 365 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER F 222 " --> pdb=" O LEU F 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE F 367 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL F 224 " --> pdb=" O PHE F 367 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP F 369 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR F 221 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS F 323 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE F 349 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 325 " --> pdb=" O PHE F 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR F 287 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL F 254 " --> pdb=" O TYR F 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 272 through 277 Processing sheet with id=AB8, first strand: chain 'G' and resid 30 through 37 Processing sheet with id=AB9, first strand: chain 'G' and resid 327 through 328 Processing sheet with id=AC1, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AC2, first strand: chain 'M' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG M 242 " --> pdb=" O VAL M 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR M 198 " --> pdb=" O THR M 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 30 through 36 removed outlier: 8.645A pdb=" N LEU N 100 " --> pdb=" O VAL N 22 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA N 24 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU N 102 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET N 26 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N PHE N 104 " --> pdb=" O MET N 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AC6, first strand: chain 'K' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR K 207 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET K 169 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU K 209 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL K 167 " --> pdb=" O LEU K 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS K 211 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET K 169 " --> pdb=" O PHE K 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE K 394 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE K 393 " --> pdb=" O THR K 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR K 376 " --> pdb=" O PHE K 393 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL K 373 " --> pdb=" O THR K 368 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU K 365 " --> pdb=" O TRP K 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER K 222 " --> pdb=" O LEU K 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE K 367 " --> pdb=" O SER K 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL K 224 " --> pdb=" O PHE K 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP K 369 " --> pdb=" O VAL K 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR K 221 " --> pdb=" O ASP K 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS K 323 " --> pdb=" O THR K 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE K 349 " --> pdb=" O HIS K 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE K 325 " --> pdb=" O PHE K 349 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR K 287 " --> pdb=" O MET K 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL K 254 " --> pdb=" O TYR K 287 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 272 through 277 Processing sheet with id=AC8, first strand: chain 'L' and resid 30 through 37 Processing sheet with id=AC9, first strand: chain 'L' and resid 327 through 328 Processing sheet with id=AD1, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD2, first strand: chain 'R' and resid 108 through 109 removed outlier: 3.541A pdb=" N ARG R 242 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR R 198 " --> pdb=" O THR R 119 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 71 through 77 removed outlier: 8.612A pdb=" N LEU S 100 " --> pdb=" O VAL S 22 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA S 24 " --> pdb=" O LEU S 100 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU S 102 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET S 26 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE S 104 " --> pdb=" O MET S 26 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 22 Processing sheet with id=AD6, first strand: chain 'P' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR P 207 " --> pdb=" O MET P 169 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET P 169 " --> pdb=" O TYR P 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU P 209 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL P 167 " --> pdb=" O LEU P 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS P 211 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET P 169 " --> pdb=" O PHE P 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE P 394 " --> pdb=" O MET P 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE P 393 " --> pdb=" O THR P 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR P 376 " --> pdb=" O PHE P 393 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL P 373 " --> pdb=" O THR P 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU P 365 " --> pdb=" O TRP P 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER P 222 " --> pdb=" O LEU P 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE P 367 " --> pdb=" O SER P 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL P 224 " --> pdb=" O PHE P 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP P 369 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR P 221 " --> pdb=" O ASP P 350 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS P 323 " --> pdb=" O THR P 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE P 349 " --> pdb=" O HIS P 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE P 325 " --> pdb=" O PHE P 349 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR P 287 " --> pdb=" O MET P 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL P 254 " --> pdb=" O TYR P 287 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 272 through 277 Processing sheet with id=AD8, first strand: chain 'Q' and resid 30 through 37 Processing sheet with id=AD9, first strand: chain 'Q' and resid 327 through 328 removed outlier: 3.647A pdb=" N LEU Q 339 " --> pdb=" O THR Q 328 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'Y' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG Y 242 " --> pdb=" O VAL Y 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 108 through 109 removed outlier: 4.336A pdb=" N THR Y 198 " --> pdb=" O THR Y 119 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 71 through 77 removed outlier: 8.746A pdb=" N LEU Z 100 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA Z 24 " --> pdb=" O LEU Z 100 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU Z 102 " --> pdb=" O ALA Z 24 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET Z 26 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE Z 104 " --> pdb=" O MET Z 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 19 through 22 Processing sheet with id=AE6, first strand: chain 'V' and resid 206 through 214 removed outlier: 6.839A pdb=" N TYR V 207 " --> pdb=" O MET V 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET V 169 " --> pdb=" O TYR V 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU V 209 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL V 167 " --> pdb=" O LEU V 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS V 211 " --> pdb=" O VAL V 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET V 169 " --> pdb=" O PHE V 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE V 394 " --> pdb=" O MET V 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE V 393 " --> pdb=" O THR V 376 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THR V 376 " --> pdb=" O PHE V 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL V 373 " --> pdb=" O THR V 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU V 365 " --> pdb=" O TRP V 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER V 222 " --> pdb=" O LEU V 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE V 367 " --> pdb=" O SER V 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL V 224 " --> pdb=" O PHE V 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP V 369 " --> pdb=" O VAL V 224 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR V 221 " --> pdb=" O ASP V 350 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS V 323 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE V 349 " --> pdb=" O HIS V 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE V 325 " --> pdb=" O PHE V 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR V 287 " --> pdb=" O MET V 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL V 254 " --> pdb=" O TYR V 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 272 through 277 Processing sheet with id=AE8, first strand: chain 'W' and resid 30 through 37 Processing sheet with id=AE9, first strand: chain '4' and resid 96 through 98 Processing sheet with id=AF1, first strand: chain '4' and resid 108 through 109 removed outlier: 3.540A pdb=" N ARG 4 242 " --> pdb=" O VAL 4 118 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 108 through 109 removed outlier: 4.337A pdb=" N THR 4 198 " --> pdb=" O THR 4 119 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '5' and resid 71 through 77 removed outlier: 8.654A pdb=" N LEU 5 100 " --> pdb=" O VAL 5 22 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA 5 24 " --> pdb=" O LEU 5 100 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU 5 102 " --> pdb=" O ALA 5 24 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET 5 26 " --> pdb=" O LEU 5 102 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N PHE 5 104 " --> pdb=" O MET 5 26 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '2' and resid 19 through 22 Processing sheet with id=AF5, first strand: chain '2' and resid 206 through 214 removed outlier: 6.840A pdb=" N TYR 2 207 " --> pdb=" O MET 2 169 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET 2 169 " --> pdb=" O TYR 2 207 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU 2 209 " --> pdb=" O VAL 2 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL 2 167 " --> pdb=" O LEU 2 209 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS 2 211 " --> pdb=" O VAL 2 165 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET 2 169 " --> pdb=" O PHE 2 394 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE 2 394 " --> pdb=" O MET 2 169 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE 2 393 " --> pdb=" O THR 2 376 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR 2 376 " --> pdb=" O PHE 2 393 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL 2 373 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU 2 365 " --> pdb=" O TRP 2 220 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER 2 222 " --> pdb=" O LEU 2 365 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE 2 367 " --> pdb=" O SER 2 222 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL 2 224 " --> pdb=" O PHE 2 367 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASP 2 369 " --> pdb=" O VAL 2 224 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR 2 221 " --> pdb=" O ASP 2 350 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS 2 323 " --> pdb=" O THR 2 347 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE 2 349 " --> pdb=" O HIS 2 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE 2 325 " --> pdb=" O PHE 2 349 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N TYR 2 287 " --> pdb=" O MET 2 252 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL 2 254 " --> pdb=" O TYR 2 287 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '2' and resid 272 through 277 Processing sheet with id=AF7, first strand: chain '3' and resid 30 through 37 Processing sheet with id=AF8, first strand: chain '3' and resid 327 through 328 4508 hydrogen bonds defined for protein. 13053 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: 30.40 Time building geometry restraints manager: 25.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23059 1.34 - 1.46: 14162 1.46 - 1.58: 35841 1.58 - 1.70: 0 1.70 - 1.82: 660 Bond restraints: 73722 Sorted by residual: bond pdb=" CB LYS W 472 " pdb=" CG LYS W 472 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C ARG Q 322 " pdb=" N PRO Q 323 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.19e-02 7.06e+03 6.32e+00 bond pdb=" CB ILE W 499 " pdb=" CG2 ILE W 499 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.00e+00 bond pdb=" CB VAL 3 407 " pdb=" CG1 VAL 3 407 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.83e+00 bond pdb=" CG1 ILE L 499 " pdb=" CD1 ILE L 499 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.34e+00 ... (remaining 73717 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.65: 2269 105.65 - 112.79: 39669 112.79 - 119.93: 25627 119.93 - 127.06: 31921 127.06 - 134.20: 1326 Bond angle restraints: 100812 Sorted by residual: angle pdb=" CA ARG L 322 " pdb=" CB ARG L 322 " pdb=" CG ARG L 322 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" C ALA 5 28 " pdb=" N ASP 5 29 " pdb=" CA ASP 5 29 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C ALA S 28 " pdb=" N ASP S 29 " pdb=" CA ASP S 29 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA ARG 3 322 " pdb=" CB ARG 3 322 " pdb=" CG ARG 3 322 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C ALA X 28 " pdb=" N ASP X 29 " pdb=" CA ASP X 29 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 ... (remaining 100807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 40620 17.98 - 35.97: 2352 35.97 - 53.95: 433 53.95 - 71.94: 88 71.94 - 89.92: 67 Dihedral angle restraints: 43560 sinusoidal: 16578 harmonic: 26982 Sorted by residual: dihedral pdb=" CA LEU G 325 " pdb=" C LEU G 325 " pdb=" N PRO G 326 " pdb=" CA PRO G 326 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PRO N 308 " pdb=" C PRO N 308 " pdb=" N VAL N 309 " pdb=" CA VAL N 309 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA PRO S 308 " pdb=" C PRO S 308 " pdb=" N VAL S 309 " pdb=" CA VAL S 309 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 43557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 9316 0.068 - 0.136: 2308 0.136 - 0.204: 365 0.204 - 0.272: 47 0.272 - 0.340: 12 Chirality restraints: 12048 Sorted by residual: chirality pdb=" CB ILE P 74 " pdb=" CA ILE P 74 " pdb=" CG1 ILE P 74 " pdb=" CG2 ILE P 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE K 74 " pdb=" CA ILE K 74 " pdb=" CG1 ILE K 74 " pdb=" CG2 ILE K 74 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 12045 not shown) Planarity restraints: 12642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP I 410 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C TRP I 410 " 0.082 2.00e-02 2.50e+03 pdb=" O TRP I 410 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN I 411 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP Z 410 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C TRP Z 410 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP Z 410 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN Z 411 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP S 410 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TRP S 410 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP S 410 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN S 411 " 0.028 2.00e-02 2.50e+03 ... (remaining 12639 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 16419 2.80 - 3.32: 73954 3.32 - 3.85: 121622 3.85 - 4.37: 135662 4.37 - 4.90: 231367 Nonbonded interactions: 579024 Sorted by model distance: nonbonded pdb=" O ALA Q 375 " pdb=" NH1 ARG Q 429 " model vdw 2.271 2.520 nonbonded pdb=" NZ LYS P 194 " pdb=" O VAL Q 309 " model vdw 2.272 2.520 nonbonded pdb=" O ALA G 375 " pdb=" NH1 ARG G 429 " model vdw 2.278 2.520 nonbonded pdb=" O ALA 3 375 " pdb=" NH1 ARG 3 429 " model vdw 2.279 2.520 nonbonded pdb=" O ALA D 375 " pdb=" NH1 ARG D 429 " model vdw 2.280 2.520 ... (remaining 579019 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 '1' selection = chain 'A' selection = chain 'B' selection = chain 'J' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'F' selection = chain 'K' selection = chain 'P' selection = chain 'V' } ncs_group { reference = (chain '3' and (resid 18 through 323 or resid 339 through 494)) selection = chain '5' selection = (chain 'D' and (resid 18 through 323 or resid 339 through 494)) selection = (chain 'G' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'I' selection = (chain 'L' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'N' selection = (chain 'Q' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'S' selection = (chain 'W' and (resid 18 through 323 or resid 339 through 494)) selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain '4' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'Y' } 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: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 20.090 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 146.410 Find NCS groups from input model: 4.460 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 73722 Z= 0.423 Angle : 1.031 13.610 100812 Z= 0.569 Chirality : 0.061 0.340 12048 Planarity : 0.008 0.092 12642 Dihedral : 12.817 89.919 26100 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.77 % Favored : 96.22 % Rotamer: Outliers : 0.37 % Allowed : 4.27 % Favored : 95.36 % Cbeta Deviations : 0.07 % 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: -0.79 (0.08), residues: 9306 helix: 0.02 (0.07), residues: 5022 sheet: -0.37 (0.17), residues: 822 loop : -1.22 (0.10), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 859 time to evaluate : 6.038 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 882 average time/residue: 0.6598 time to fit residues: 999.6497 Evaluate side-chains 556 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 540 time to evaluate : 6.111 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5083 time to fit residues: 23.4107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 785 optimal weight: 9.9990 chunk 704 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 475 optimal weight: 20.0000 chunk 376 optimal weight: 0.6980 chunk 728 optimal weight: 8.9990 chunk 282 optimal weight: 0.8980 chunk 443 optimal weight: 3.9990 chunk 542 optimal weight: 6.9990 chunk 844 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 ASN ** K 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 293 HIS ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 20 ASN ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 73722 Z= 0.286 Angle : 0.681 13.028 100812 Z= 0.347 Chirality : 0.045 0.301 12048 Planarity : 0.005 0.059 12642 Dihedral : 5.223 51.023 10224 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.63 % Allowed : 9.22 % Favored : 89.15 % 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: 0.67 (0.09), residues: 9306 helix: 1.48 (0.07), residues: 5148 sheet: -0.21 (0.16), residues: 924 loop : -1.00 (0.11), residues: 3234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 616 time to evaluate : 5.910 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 outliers start: 123 outliers final: 51 residues processed: 699 average time/residue: 0.6341 time to fit residues: 778.9802 Evaluate side-chains 559 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 508 time to evaluate : 7.242 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.5592 time to fit residues: 61.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 469 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 702 optimal weight: 0.7980 chunk 575 optimal weight: 30.0000 chunk 232 optimal weight: 0.6980 chunk 846 optimal weight: 0.8980 chunk 913 optimal weight: 2.9990 chunk 753 optimal weight: 4.9990 chunk 839 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 678 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 293 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 ASN ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 73722 Z= 0.199 Angle : 0.619 13.224 100812 Z= 0.309 Chirality : 0.043 0.247 12048 Planarity : 0.005 0.056 12642 Dihedral : 4.740 44.037 10224 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.04 % Allowed : 10.86 % Favored : 87.10 % 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: 1.11 (0.09), residues: 9306 helix: 1.88 (0.07), residues: 5130 sheet: -0.34 (0.17), residues: 870 loop : -0.78 (0.11), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 572 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 55 residues processed: 687 average time/residue: 0.6379 time to fit residues: 778.8171 Evaluate side-chains 542 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 487 time to evaluate : 6.029 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.5450 time to fit residues: 63.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 835 optimal weight: 10.0000 chunk 636 optimal weight: 3.9990 chunk 439 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 403 optimal weight: 8.9990 chunk 568 optimal weight: 20.0000 chunk 849 optimal weight: 6.9990 chunk 898 optimal weight: 0.0870 chunk 443 optimal weight: 5.9990 chunk 804 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 197 HIS ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 73722 Z= 0.223 Angle : 0.612 10.617 100812 Z= 0.305 Chirality : 0.043 0.227 12048 Planarity : 0.004 0.054 12642 Dihedral : 4.549 35.667 10224 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.50 % Allowed : 12.61 % Favored : 85.89 % 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: 1.26 (0.09), residues: 9306 helix: 2.02 (0.07), residues: 5082 sheet: -0.30 (0.16), residues: 918 loop : -0.69 (0.12), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 546 time to evaluate : 6.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 62 residues processed: 632 average time/residue: 0.6207 time to fit residues: 698.7483 Evaluate side-chains 557 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 495 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5906 time to fit residues: 74.7418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 748 optimal weight: 1.9990 chunk 510 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 669 optimal weight: 3.9990 chunk 370 optimal weight: 7.9990 chunk 767 optimal weight: 0.9990 chunk 621 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 459 optimal weight: 0.7980 chunk 806 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 GLN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 333 GLN L 31 GLN J 52 GLN ** P 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 73722 Z= 0.215 Angle : 0.613 11.043 100812 Z= 0.303 Chirality : 0.043 0.355 12048 Planarity : 0.004 0.053 12642 Dihedral : 4.421 27.608 10224 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.95 % Allowed : 14.20 % Favored : 84.84 % 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: 1.29 (0.09), residues: 9306 helix: 2.07 (0.07), residues: 5088 sheet: -0.36 (0.16), residues: 984 loop : -0.72 (0.12), residues: 3234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 537 time to evaluate : 6.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 34 residues processed: 593 average time/residue: 0.6155 time to fit residues: 648.3231 Evaluate side-chains 530 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 496 time to evaluate : 5.986 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5316 time to fit residues: 42.6989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 302 optimal weight: 1.9990 chunk 809 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 chunk 527 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 899 optimal weight: 4.9990 chunk 746 optimal weight: 2.9990 chunk 416 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 chunk 472 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 73722 Z= 0.199 Angle : 0.613 12.250 100812 Z= 0.300 Chirality : 0.043 0.423 12048 Planarity : 0.004 0.053 12642 Dihedral : 4.290 22.023 10224 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.86 % Allowed : 15.43 % Favored : 83.70 % 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: 1.29 (0.09), residues: 9306 helix: 2.10 (0.07), residues: 5088 sheet: -0.41 (0.16), residues: 984 loop : -0.75 (0.12), residues: 3234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 548 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 32 residues processed: 592 average time/residue: 0.6287 time to fit residues: 658.0325 Evaluate side-chains 543 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 511 time to evaluate : 6.087 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5488 time to fit residues: 40.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 867 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 512 optimal weight: 10.0000 chunk 657 optimal weight: 10.0000 chunk 509 optimal weight: 8.9990 chunk 757 optimal weight: 9.9990 chunk 502 optimal weight: 6.9990 chunk 896 optimal weight: 0.7980 chunk 560 optimal weight: 10.0000 chunk 546 optimal weight: 2.9990 chunk 413 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 293 HIS ** 2 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 73722 Z= 0.567 Angle : 0.845 13.580 100812 Z= 0.425 Chirality : 0.049 0.458 12048 Planarity : 0.006 0.061 12642 Dihedral : 4.999 25.907 10224 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.34 % Allowed : 15.59 % Favored : 83.07 % 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: 0.39 (0.09), residues: 9306 helix: 1.23 (0.07), residues: 5172 sheet: -0.65 (0.16), residues: 972 loop : -1.01 (0.11), residues: 3162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 480 time to evaluate : 6.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 63 residues processed: 543 average time/residue: 0.6235 time to fit residues: 598.5512 Evaluate side-chains 526 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 463 time to evaluate : 5.983 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5713 time to fit residues: 72.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 554 optimal weight: 8.9990 chunk 357 optimal weight: 8.9990 chunk 535 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 569 optimal weight: 0.7980 chunk 610 optimal weight: 1.9990 chunk 443 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 704 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 31 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 GLN F 333 GLN G 125 ASN ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 ASN ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 240 GLN W 125 ASN T 52 GLN 2 333 GLN ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 73722 Z= 0.249 Angle : 0.660 14.539 100812 Z= 0.323 Chirality : 0.043 0.446 12048 Planarity : 0.004 0.051 12642 Dihedral : 4.590 23.821 10224 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.36 % Allowed : 16.84 % Favored : 82.80 % 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: 0.88 (0.09), residues: 9306 helix: 1.75 (0.07), residues: 5136 sheet: -0.65 (0.17), residues: 918 loop : -0.90 (0.11), residues: 3252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 519 time to evaluate : 6.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 536 average time/residue: 0.6297 time to fit residues: 596.3234 Evaluate side-chains 509 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 497 time to evaluate : 5.957 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5622 time to fit residues: 20.2712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 815 optimal weight: 10.0000 chunk 858 optimal weight: 9.9990 chunk 783 optimal weight: 10.0000 chunk 835 optimal weight: 3.9990 chunk 502 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 chunk 655 optimal weight: 0.6980 chunk 256 optimal weight: 9.9990 chunk 754 optimal weight: 0.6980 chunk 790 optimal weight: 9.9990 chunk 832 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 73722 Z= 0.390 Angle : 0.738 16.140 100812 Z= 0.364 Chirality : 0.046 0.504 12048 Planarity : 0.005 0.053 12642 Dihedral : 4.718 24.045 10224 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.45 % Allowed : 17.14 % Favored : 82.41 % 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: 0.65 (0.09), residues: 9306 helix: 1.55 (0.07), residues: 5160 sheet: -0.76 (0.16), residues: 972 loop : -1.02 (0.11), residues: 3174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 491 time to evaluate : 6.424 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 outliers start: 34 outliers final: 24 residues processed: 515 average time/residue: 0.6447 time to fit residues: 587.9627 Evaluate side-chains 507 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 483 time to evaluate : 6.064 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5339 time to fit residues: 32.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 548 optimal weight: 8.9990 chunk 883 optimal weight: 0.9980 chunk 539 optimal weight: 8.9990 chunk 419 optimal weight: 20.0000 chunk 614 optimal weight: 0.9980 chunk 926 optimal weight: 0.8980 chunk 852 optimal weight: 7.9990 chunk 737 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 569 optimal weight: 10.0000 chunk 452 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 73722 Z= 0.197 Angle : 0.652 17.063 100812 Z= 0.316 Chirality : 0.043 0.533 12048 Planarity : 0.004 0.054 12642 Dihedral : 4.399 21.394 10224 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.21 % Allowed : 17.67 % Favored : 82.11 % 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: 1.01 (0.09), residues: 9306 helix: 1.90 (0.07), residues: 5160 sheet: -0.72 (0.17), residues: 912 loop : -0.92 (0.12), residues: 3234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18612 Ramachandran restraints generated. 9306 Oldfield, 0 Emsley, 9306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 528 time to evaluate : 6.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 536 average time/residue: 0.6503 time to fit residues: 617.5234 Evaluate side-chains 517 residues out of total 7542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 507 time to evaluate : 6.096 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5612 time to fit residues: 18.3481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 930 random chunks: chunk 586 optimal weight: 0.3980 chunk 785 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 680 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 205 optimal weight: 0.0470 chunk 738 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 758 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 399 GLN ** 2 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.087739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.067894 restraints weight = 354826.459| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.82 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 73722 Z= 0.164 Angle : 0.637 16.740 100812 Z= 0.306 Chirality : 0.043 0.540 12048 Planarity : 0.004 0.055 12642 Dihedral : 4.158 19.786 10224 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.13 % Allowed : 17.63 % Favored : 82.23 % 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: 1.17 (0.09), residues: 9306 helix: 2.05 (0.07), residues: 5136 sheet: -0.65 (0.16), residues: 948 loop : -0.88 (0.12), residues: 3222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13226.00 seconds wall clock time: 234 minutes 38.28 seconds (14078.28 seconds total)