Starting phenix.real_space_refine (version: dev) on Fri Apr 8 02:56:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pof_20414/04_2022/6pof_20414_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ASP 644": "OD1" <-> "OD2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ASP 1026": "OD1" <-> "OD2" Residue "A ARG 1045": "NH1" <-> "NH2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B ASP 46": "OD1" <-> "OD2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ASP 644": "OD1" <-> "OD2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ASP 803": "OD1" <-> "OD2" Residue "B PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 891": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1045": "NH1" <-> "NH2" Residue "B GLU 1050": "OE1" <-> "OE2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "C ASP 644": "OD1" <-> "OD2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 690": "OD1" <-> "OD2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ASP 803": "OD1" <-> "OD2" Residue "C GLU 815": "OE1" <-> "OE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C GLU 1050": "OE1" <-> "OE2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D ASP 514": "OD1" <-> "OD2" Residue "D TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 547": "OE1" <-> "OE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D ASP 644": "OD1" <-> "OD2" Residue "D TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ASP 803": "OD1" <-> "OD2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D ASP 1026": "OD1" <-> "OD2" Residue "D ARG 1045": "NH1" <-> "NH2" Residue "D GLU 1050": "OE1" <-> "OE2" Residue "D ARG 1085": "NH1" <-> "NH2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 31624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 971, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Time building chain proxies: 30.20, per 1000 atoms: 0.95 Number of scatterers: 31624 At special positions: 0 Unit cell: (152.955, 176.715, 158.895, 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 176 16.00 O 5832 8.00 N 5360 7.00 C 20256 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: 11.79 Conformation dependent library (CDL) restraints added in 8.5 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 32 sheets defined 43.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.649A pdb=" N TYR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.204A pdb=" N LEU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.621A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.768A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.182A pdb=" N ASP A 141 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.703A pdb=" N ILE A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.623A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 6.630A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.524A pdb=" N ILE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.091A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.645A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.872A pdb=" N ARG A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.506A pdb=" N GLU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.102A pdb=" N GLY A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.841A pdb=" N GLY A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 removed outlier: 4.607A pdb=" N PHE A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 removed outlier: 3.523A pdb=" N MET A 560 " --> pdb=" O MET A 556 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.557A pdb=" N SER A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.819A pdb=" N GLU A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.775A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 4.202A pdb=" N ILE A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.545A pdb=" N ASN A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.558A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.590A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.975A pdb=" N LYS A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 783 removed outlier: 3.541A pdb=" N GLY A 783 " --> pdb=" O LYS A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 792 through 805 removed outlier: 3.501A pdb=" N ILE A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 removed outlier: 3.597A pdb=" N LEU A 831 " --> pdb=" O TRP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.674A pdb=" N VAL A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 removed outlier: 3.652A pdb=" N TRP A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 896 removed outlier: 3.504A pdb=" N VAL A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 removed outlier: 4.033A pdb=" N ASN A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.632A pdb=" N THR A 930 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 931 " --> pdb=" O LEU A 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 927 through 931' Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.559A pdb=" N ALA A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 Processing helix chain 'A' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 997 removed outlier: 3.640A pdb=" N ASP A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 997 " --> pdb=" O TYR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.846A pdb=" N ASP A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1033 Processing helix chain 'A' and resid 1033 through 1038 Processing helix chain 'A' and resid 1046 through 1055 removed outlier: 3.882A pdb=" N GLU A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A1055 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 3.573A pdb=" N GLY A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A1066 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.673A pdb=" N TYR B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 47 removed outlier: 4.208A pdb=" N LEU B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.599A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.773A pdb=" N LYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.159A pdb=" N ASP B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.705A pdb=" N ILE B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.624A pdb=" N PHE B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 6.623A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.546A pdb=" N ILE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.087A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.632A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.884A pdb=" N ARG B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 399 removed outlier: 4.124A pdb=" N GLY B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 removed outlier: 3.814A pdb=" N GLY B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 removed outlier: 4.595A pdb=" N PHE B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 removed outlier: 3.522A pdb=" N MET B 560 " --> pdb=" O MET B 556 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.527A pdb=" N SER B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 578' Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.884A pdb=" N GLU B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 removed outlier: 3.774A pdb=" N LEU B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 611 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 649 removed outlier: 4.197A pdb=" N ILE B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.755A pdb=" N SER B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 676 " --> pdb=" O ASN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.520A pdb=" N VAL B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.980A pdb=" N LYS B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 779 " --> pdb=" O LYS B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 783 removed outlier: 3.575A pdb=" N GLY B 783 " --> pdb=" O LYS B 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 780 through 783' Processing helix chain 'B' and resid 792 through 805 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.602A pdb=" N LEU B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 866 removed outlier: 3.661A pdb=" N VAL B 862 " --> pdb=" O PRO B 858 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 863 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 864 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 879 removed outlier: 3.653A pdb=" N TRP B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.517A pdb=" N VAL B 896 " --> pdb=" O MET B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 916 removed outlier: 4.080A pdb=" N ASN B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 910 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 912 " --> pdb=" O HIS B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.732A pdb=" N THR B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.556A pdb=" N THR B 930 " --> pdb=" O GLY B 927 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 931 " --> pdb=" O LEU B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 931' Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.572A pdb=" N ALA B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 952 Processing helix chain 'B' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 997 removed outlier: 3.639A pdb=" N ASP B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 993 " --> pdb=" O ILE B 989 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS B 997 " --> pdb=" O TYR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.852A pdb=" N ASP B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B1013 " --> pdb=" O GLU B1009 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B1016 " --> pdb=" O LYS B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1033 Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1046 through 1055 removed outlier: 3.745A pdb=" N GLU B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B1051 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1079 removed outlier: 3.573A pdb=" N GLY B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B1066 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B1070 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.654A pdb=" N TYR C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.205A pdb=" N LEU C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.588A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 77 through 85 removed outlier: 3.725A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 161 through 168 removed outlier: 3.704A pdb=" N ILE C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.631A pdb=" N PHE C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 6.596A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.503A pdb=" N ALA C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 312 through 327 removed outlier: 4.153A pdb=" N ILE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.648A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.866A pdb=" N ARG C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.510A pdb=" N GLU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 4.104A pdb=" N GLY C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 419 removed outlier: 3.826A pdb=" N GLY C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 removed outlier: 4.611A pdb=" N PHE C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 removed outlier: 3.521A pdb=" N MET C 560 " --> pdb=" O MET C 556 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 578 removed outlier: 3.534A pdb=" N SER C 577 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 574 through 578' Processing helix chain 'C' and resid 579 through 584 removed outlier: 3.862A pdb=" N GLU C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 removed outlier: 3.777A pdb=" N LEU C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS C 611 " --> pdb=" O ARG C 607 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 615 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 649 removed outlier: 4.190A pdb=" N ILE C 646 " --> pdb=" O MET C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 675 removed outlier: 3.581A pdb=" N ASN C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 removed outlier: 3.572A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.607A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 779 removed outlier: 4.051A pdb=" N LYS C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 779 " --> pdb=" O LYS C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 783 removed outlier: 3.525A pdb=" N GLY C 783 " --> pdb=" O LYS C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 780 through 783' Processing helix chain 'C' and resid 792 through 805 Processing helix chain 'C' and resid 825 through 831 removed outlier: 3.612A pdb=" N LEU C 831 " --> pdb=" O TRP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 3.656A pdb=" N VAL C 862 " --> pdb=" O PRO C 858 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 863 " --> pdb=" O ILE C 859 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 864 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 879 removed outlier: 3.716A pdb=" N TRP C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 897 removed outlier: 3.547A pdb=" N VAL C 896 " --> pdb=" O MET C 892 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 897 " --> pdb=" O CYS C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 916 removed outlier: 4.062A pdb=" N ASN C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 912 " --> pdb=" O HIS C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 removed outlier: 3.648A pdb=" N THR C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.534A pdb=" N LEU C 929 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 930 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 931 " --> pdb=" O LEU C 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 926 through 931' Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 947 through 952 Processing helix chain 'C' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.639A pdb=" N ASP C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 993 " --> pdb=" O ILE C 989 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS C 997 " --> pdb=" O TYR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.837A pdb=" N ASP C1005 " --> pdb=" O THR C1001 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C1009 " --> pdb=" O ASP C1005 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C1013 " --> pdb=" O GLU C1009 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1033 Processing helix chain 'C' and resid 1033 through 1038 Processing helix chain 'C' and resid 1046 through 1055 removed outlier: 3.722A pdb=" N GLU C1050 " --> pdb=" O GLU C1046 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 3.567A pdb=" N GLY C1059 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C1066 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C1070 " --> pdb=" O SER C1066 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C1071 " --> pdb=" O MET C1067 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C1079 " --> pdb=" O ASP C1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.664A pdb=" N TYR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 47 removed outlier: 4.207A pdb=" N LEU D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.628A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.770A pdb=" N LYS D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 138 through 142 removed outlier: 4.155A pdb=" N ASP D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 142 " --> pdb=" O GLY D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 142' Processing helix chain 'D' and resid 161 through 168 removed outlier: 3.701A pdb=" N ILE D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.638A pdb=" N PHE D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.607A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.540A pdb=" N ILE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'D' and resid 312 through 327 removed outlier: 4.082A pdb=" N ILE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 354 removed outlier: 3.669A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.883A pdb=" N ARG D 362 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 383 through 399 removed outlier: 4.117A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 419 removed outlier: 3.816A pdb=" N GLY D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 519 removed outlier: 4.593A pdb=" N PHE D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 516 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 removed outlier: 3.522A pdb=" N MET D 560 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.566A pdb=" N SER D 577 " --> pdb=" O SER D 574 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 574 through 578' Processing helix chain 'D' and resid 579 through 584 removed outlier: 3.879A pdb=" N GLU D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 removed outlier: 3.782A pdb=" N LEU D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS D 611 " --> pdb=" O ARG D 607 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 649 removed outlier: 4.232A pdb=" N ILE D 646 " --> pdb=" O MET D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.745A pdb=" N SER D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 676 " --> pdb=" O ASN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.557A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.581A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 779 removed outlier: 3.975A pdb=" N LYS D 775 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 779 " --> pdb=" O LYS D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 783 removed outlier: 3.571A pdb=" N GLY D 783 " --> pdb=" O LYS D 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 780 through 783' Processing helix chain 'D' and resid 792 through 805 Processing helix chain 'D' and resid 825 through 831 removed outlier: 3.692A pdb=" N LEU D 831 " --> pdb=" O TRP D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 866 removed outlier: 3.672A pdb=" N VAL D 862 " --> pdb=" O PRO D 858 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 879 removed outlier: 3.502A pdb=" N VAL D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP D 877 " --> pdb=" O LEU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 897 removed outlier: 3.511A pdb=" N VAL D 896 " --> pdb=" O MET D 892 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 897 " --> pdb=" O CYS D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 removed outlier: 4.062A pdb=" N ASN D 909 " --> pdb=" O SER D 905 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 910 " --> pdb=" O GLY D 906 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 912 " --> pdb=" O HIS D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.552A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 952 Processing helix chain 'D' and resid 955 through 964 removed outlier: 5.124A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 997 removed outlier: 3.648A pdb=" N ASP D 992 " --> pdb=" O GLN D 988 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 993 " --> pdb=" O ILE D 989 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D 997 " --> pdb=" O TYR D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.851A pdb=" N ASP D1005 " --> pdb=" O THR D1001 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D1013 " --> pdb=" O GLU D1009 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1033 Processing helix chain 'D' and resid 1033 through 1038 Processing helix chain 'D' and resid 1046 through 1055 removed outlier: 3.720A pdb=" N GLU D1050 " --> pdb=" O GLU D1046 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D1051 " --> pdb=" O GLU D1047 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY D1055 " --> pdb=" O TYR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1079 removed outlier: 3.557A pdb=" N GLY D1059 " --> pdb=" O GLY D1055 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER D1066 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D1070 " --> pdb=" O SER D1066 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D1071 " --> pdb=" O MET D1067 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.630A pdb=" N VAL A 221 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 121 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE A 119 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.630A pdb=" N VAL A 221 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.419A pdb=" N LEU A 55 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 75 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 268 removed outlier: 4.129A pdb=" N VAL A 279 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 307 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.368A pdb=" N TRP A 276 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 374 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS A 403 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 375 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE A 405 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 377 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 541 removed outlier: 7.111A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 500 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 595 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 571 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.721A pdb=" N VAL A 657 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 685 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 659 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL B 221 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 121 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE B 119 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL B 221 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.405A pdb=" N LEU B 55 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 75 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 268 removed outlier: 4.144A pdb=" N VAL B 279 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 307 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.410A pdb=" N TRP B 276 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N HIS B 403 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 375 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE B 405 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 377 " --> pdb=" O PHE B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 537 through 541 removed outlier: 7.105A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 500 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 595 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 571 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 634 through 635 removed outlier: 6.519A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.626A pdb=" N VAL C 221 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 121 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 119 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.626A pdb=" N VAL C 221 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.810A pdb=" N LEU C 55 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 75 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 268 removed outlier: 4.086A pdb=" N VAL C 279 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 307 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.354A pdb=" N TRP C 276 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N HIS C 403 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 375 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE C 405 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 377 " --> pdb=" O PHE C 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 537 through 541 removed outlier: 7.096A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 500 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 595 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 571 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.516A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL D 221 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 121 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE D 119 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL D 221 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.406A pdb=" N LEU D 55 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN D 75 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD2, first strand: chain 'D' and resid 264 through 268 removed outlier: 4.161A pdb=" N VAL D 279 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR D 307 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.406A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N HIS D 403 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE D 375 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE D 405 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 377 " --> pdb=" O PHE D 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 537 through 541 removed outlier: 7.099A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 500 " --> pdb=" O ILE D 570 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 595 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 571 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 634 through 635 removed outlier: 6.515A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2949 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: 12.69 Time building geometry restraints manager: 12.76 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: 9993 1.34 - 1.46: 6715 1.46 - 1.58: 15320 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 32316 Sorted by residual: bond pdb=" C LYS C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.08e+01 bond pdb=" C LYS A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.03e+01 bond pdb=" C LYS D 86 " pdb=" N PRO D 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.02e+01 bond pdb=" N THR B 842 " pdb=" CA THR B 842 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.82e+00 bond pdb=" N THR D 842 " pdb=" CA THR D 842 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.66e+00 ... (remaining 32311 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.35: 1003 106.35 - 113.33: 17442 113.33 - 120.32: 12743 120.32 - 127.30: 12256 127.30 - 134.29: 316 Bond angle restraints: 43760 Sorted by residual: angle pdb=" C MET D 823 " pdb=" N ASP D 824 " pdb=" CA ASP D 824 " ideal model delta sigma weight residual 121.54 133.89 -12.35 1.91e+00 2.74e-01 4.18e+01 angle pdb=" C ILE D 834 " pdb=" N ARG D 835 " pdb=" CA ARG D 835 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ILE A 834 " pdb=" N ARG A 835 " pdb=" CA ARG A 835 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ILE B 834 " pdb=" N ARG B 835 " pdb=" CA ARG B 835 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ILE C 834 " pdb=" N ARG C 835 " pdb=" CA ARG C 835 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.83e+01 ... (remaining 43755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 17253 17.34 - 34.68: 1696 34.68 - 52.02: 286 52.02 - 69.35: 52 69.35 - 86.69: 33 Dihedral angle restraints: 19320 sinusoidal: 7680 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY C 622 " pdb=" C GLY C 622 " pdb=" N PRO C 623 " pdb=" CA PRO C 623 " ideal model delta harmonic sigma weight residual -180.00 -141.34 -38.66 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA GLY A 622 " pdb=" C GLY A 622 " pdb=" N PRO A 623 " pdb=" CA PRO A 623 " ideal model delta harmonic sigma weight residual 180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA GLY D 622 " pdb=" C GLY D 622 " pdb=" N PRO D 623 " pdb=" CA PRO D 623 " ideal model delta harmonic sigma weight residual 180.00 -141.40 -38.60 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 19317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4222 0.082 - 0.164: 627 0.164 - 0.246: 32 0.246 - 0.328: 7 0.328 - 0.411: 4 Chirality restraints: 4892 Sorted by residual: chirality pdb=" CB ILE C 834 " pdb=" CA ILE C 834 " pdb=" CG1 ILE C 834 " pdb=" CG2 ILE C 834 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE B 834 " pdb=" CA ILE B 834 " pdb=" CG1 ILE B 834 " pdb=" CG2 ILE B 834 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB ILE A 834 " pdb=" CA ILE A 834 " pdb=" CG1 ILE A 834 " pdb=" CG2 ILE A 834 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 4889 not shown) Planarity restraints: 5612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 35 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO C 36 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 35 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO B 36 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 35 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO D 36 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " 0.040 5.00e-02 4.00e+02 ... (remaining 5609 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3042 2.74 - 3.28: 29955 3.28 - 3.82: 52264 3.82 - 4.36: 60978 4.36 - 4.90: 99911 Nonbonded interactions: 246150 Sorted by model distance: nonbonded pdb=" OG1 THR B 925 " pdb=" OG1 THR D 925 " model vdw 2.196 2.440 nonbonded pdb=" O GLY C 622 " pdb=" OG1 THR C 625 " model vdw 2.247 2.440 nonbonded pdb=" O VAL A 921 " pdb=" OG1 THR A 925 " model vdw 2.249 2.440 nonbonded pdb=" O GLY D 622 " pdb=" OG1 THR D 625 " model vdw 2.252 2.440 nonbonded pdb=" O GLY B 622 " pdb=" OG1 THR B 625 " model vdw 2.253 2.440 ... (remaining 246145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 20256 2.51 5 N 5360 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.800 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.270 Process input model: 95.870 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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 0.055 32316 Z= 0.378 Angle : 0.951 12.353 43760 Z= 0.530 Chirality : 0.057 0.411 4892 Planarity : 0.007 0.072 5612 Dihedral : 14.301 86.693 11928 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.33 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.10), residues: 4068 helix: -4.19 (0.07), residues: 1544 sheet: -1.54 (0.21), residues: 472 loop : -2.97 (0.11), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 524 time to evaluate : 3.893 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 outliers start: 5 outliers final: 1 residues processed: 529 average time/residue: 0.4547 time to fit residues: 372.7614 Evaluate side-chains 315 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2623 time to fit residues: 5.3716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 chunk 171 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 319 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN A 150 GLN A 190 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 961 ASN A1076 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 150 GLN B 190 ASN B 315 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 961 ASN B1076 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 54 ASN C 75 ASN C 150 GLN C 168 HIS C 190 ASN C 671 ASN C 850 GLN C 961 ASN C1072 HIS C1076 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 150 GLN D 190 ASN D 332 HIS D 671 ASN D 705 GLN D 850 GLN D 961 ASN D1072 HIS D1076 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 32316 Z= 0.328 Angle : 0.735 12.406 43760 Z= 0.389 Chirality : 0.049 0.285 4892 Planarity : 0.006 0.057 5612 Dihedral : 6.364 32.569 4428 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.66 % Favored : 92.24 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.11), residues: 4068 helix: -2.84 (0.10), residues: 1664 sheet: -1.19 (0.22), residues: 484 loop : -2.81 (0.12), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 450 time to evaluate : 3.451 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 outliers start: 2 outliers final: 0 residues processed: 452 average time/residue: 0.4141 time to fit residues: 308.8268 Evaluate side-chains 308 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 102 optimal weight: 40.0000 chunk 371 optimal weight: 30.0000 chunk 400 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 40.0000 chunk 126 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 908 HIS ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS C 9 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 GLN D 908 HIS D1020 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 32316 Z= 0.253 Angle : 0.666 10.602 43760 Z= 0.350 Chirality : 0.047 0.193 4892 Planarity : 0.005 0.058 5612 Dihedral : 5.943 31.971 4428 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.14 % Favored : 92.76 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.12), residues: 4068 helix: -2.01 (0.11), residues: 1664 sheet: -1.02 (0.22), residues: 480 loop : -2.61 (0.12), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 3.670 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 outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3847 time to fit residues: 269.0113 Evaluate side-chains 307 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 177 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 30.0000 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 0.6980 chunk 106 optimal weight: 30.0000 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN B 9 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS D 9 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 32316 Z= 0.210 Angle : 0.630 11.500 43760 Z= 0.329 Chirality : 0.046 0.181 4892 Planarity : 0.004 0.050 5612 Dihedral : 5.653 30.816 4428 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.23 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 4068 helix: -1.59 (0.12), residues: 1684 sheet: -0.93 (0.22), residues: 480 loop : -2.49 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.614 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 outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.4018 time to fit residues: 269.9890 Evaluate side-chains 298 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 0.0170 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.135 32316 Z= 0.220 Angle : 0.633 10.597 43760 Z= 0.331 Chirality : 0.046 0.307 4892 Planarity : 0.005 0.068 5612 Dihedral : 5.454 29.690 4428 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.43 % Favored : 93.47 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.12), residues: 4068 helix: -1.28 (0.12), residues: 1676 sheet: -0.73 (0.23), residues: 472 loop : -2.33 (0.13), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 3.600 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 outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.3866 time to fit residues: 247.5042 Evaluate side-chains 301 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 20.0000 chunk 355 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 20.0000 chunk 182 optimal weight: 0.3980 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 410 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 32316 Z= 0.225 Angle : 0.639 8.273 43760 Z= 0.331 Chirality : 0.047 0.325 4892 Planarity : 0.004 0.048 5612 Dihedral : 5.392 30.426 4428 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.88 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 4068 helix: -1.12 (0.12), residues: 1688 sheet: -0.68 (0.23), residues: 476 loop : -2.24 (0.13), residues: 1904 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.067 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: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4022 time to fit residues: 244.4146 Evaluate side-chains 277 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 30.0000 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 705 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 32316 Z= 0.250 Angle : 0.654 8.305 43760 Z= 0.338 Chirality : 0.048 0.337 4892 Planarity : 0.004 0.047 5612 Dihedral : 5.382 29.887 4428 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.12), residues: 4068 helix: -1.01 (0.12), residues: 1664 sheet: -0.67 (0.23), residues: 476 loop : -2.18 (0.13), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.655 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 outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.4074 time to fit residues: 244.2910 Evaluate side-chains 282 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 0.0370 chunk 234 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 309 optimal weight: 7.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.389 32316 Z= 0.249 Angle : 0.637 20.829 43760 Z= 0.331 Chirality : 0.047 0.318 4892 Planarity : 0.004 0.081 5612 Dihedral : 5.226 30.018 4428 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.18 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.13), residues: 4068 helix: -0.84 (0.13), residues: 1652 sheet: -0.57 (0.23), residues: 476 loop : -2.09 (0.13), residues: 1940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.681 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 outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.4045 time to fit residues: 249.6297 Evaluate side-chains 281 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 0.0470 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 4.9990 overall best weight: 2.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.153 32316 Z= 0.206 Angle : 0.629 13.214 43760 Z= 0.324 Chirality : 0.047 0.358 4892 Planarity : 0.004 0.063 5612 Dihedral : 5.124 30.080 4428 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.95 % Favored : 92.96 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 4068 helix: -0.75 (0.13), residues: 1648 sheet: -0.48 (0.23), residues: 476 loop : -1.99 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.003 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: 0 outliers final: 0 residues processed: 357 average time/residue: 0.4071 time to fit residues: 242.4323 Evaluate side-chains 277 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 0.0030 chunk 236 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 0.2980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.183 32316 Z= 0.196 Angle : 0.629 18.321 43760 Z= 0.324 Chirality : 0.047 0.359 4892 Planarity : 0.005 0.172 5612 Dihedral : 4.965 27.403 4428 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.16 % Favored : 93.74 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.80 (0.13), residues: 4068 helix: -0.61 (0.13), residues: 1632 sheet: -0.42 (0.23), residues: 476 loop : -1.89 (0.13), residues: 1960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.707 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 outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3985 time to fit residues: 242.3567 Evaluate side-chains 291 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.0970 chunk 344 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.158237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.142361 restraints weight = 165962.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.140604 restraints weight = 147440.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.137900 restraints weight = 120215.660| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4380 r_free = 0.4380 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4379 r_free = 0.4379 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.150 32316 Z= 0.209 Angle : 0.640 15.622 43760 Z= 0.327 Chirality : 0.047 0.363 4892 Planarity : 0.005 0.141 5612 Dihedral : 4.965 27.366 4428 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.28 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.78 (0.13), residues: 4068 helix: -0.62 (0.13), residues: 1648 sheet: -0.36 (0.24), residues: 468 loop : -1.87 (0.13), residues: 1952 =============================================================================== Job complete usr+sys time: 5658.55 seconds wall clock time: 104 minutes 54.49 seconds (6294.49 seconds total)