Starting phenix.real_space_refine on Sun Feb 18 13:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2024/7wf3_32459_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.041 sd= 1.215 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 116 5.16 5 C 14164 2.51 5 N 3720 2.21 5 O 4084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 489": "NH1" <-> "NH2" Residue "F PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 489": "NH1" <-> "NH2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 298": "NH1" <-> "NH2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H GLU 258": "OE1" <-> "OE2" Residue "H ARG 313": "NH1" <-> "NH2" Residue "H PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "H ARG 350": "NH1" <-> "NH2" Residue "H ARG 373": "NH1" <-> "NH2" Residue "H PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 489": "NH1" <-> "NH2" Residue "I ASP 85": "OD1" <-> "OD2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 298": "NH1" <-> "NH2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 146": "OE1" <-> "OE2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J ARG 198": "NH1" <-> "NH2" Residue "J PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 85": "OD1" <-> "OD2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 298": "NH1" <-> "NH2" Residue "N PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 150": "OD1" <-> "OD2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "N ARG 198": "NH1" <-> "NH2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 146": "OE1" <-> "OE2" Residue "O PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O GLU 183": "OE1" <-> "OE2" Residue "O ARG 198": "NH1" <-> "NH2" Residue "O PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 146": "OE1" <-> "OE2" Residue "P PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 150": "OD1" <-> "OD2" Residue "P GLU 183": "OE1" <-> "OE2" Residue "P ARG 198": "NH1" <-> "NH2" Residue "P PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22100 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "C" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "F" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Time building chain proxies: 10.84, per 1000 atoms: 0.49 Number of scatterers: 22100 At special positions: 0 Unit cell: (131.274, 131.274, 159.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 116 16.00 P 12 15.00 O 4084 8.00 N 3720 7.00 C 14164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 123 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 123 " distance=2.03 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: 8.27 Conformation dependent library (CDL) restraints added in 3.7 seconds 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 16 sheets defined 55.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 231 through 255 removed outlier: 4.677A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 315 removed outlier: 3.829A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 300 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 328 through 351 removed outlier: 3.594A pdb=" N ILE B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 360 through 379 removed outlier: 3.604A pdb=" N ARG B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE B 375 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 392 Processing helix chain 'B' and resid 395 through 420 Processing helix chain 'B' and resid 431 through 441 removed outlier: 3.572A pdb=" N PHE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 441 " --> pdb=" O TRP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 4.004A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.175A pdb=" N GLU B 490 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 491 " --> pdb=" O TYR B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 90 through 106 removed outlier: 6.313A pdb=" N ALA C 95 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 106 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 192 through 204 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 229 through 235 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.973A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.881A pdb=" N GLY C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 231 through 255 removed outlier: 4.676A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 315 removed outlier: 3.829A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 300 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 328 through 351 removed outlier: 3.594A pdb=" N ILE D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 360 through 379 removed outlier: 3.604A pdb=" N ARG D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU D 377 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG D 379 " --> pdb=" O PHE D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 395 through 420 Processing helix chain 'D' and resid 431 through 441 removed outlier: 3.571A pdb=" N PHE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 473 removed outlier: 4.003A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 491 removed outlier: 4.176A pdb=" N GLU D 490 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR D 491 " --> pdb=" O TYR D 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 225 Processing helix chain 'F' and resid 231 through 255 removed outlier: 4.676A pdb=" N THR F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 315 removed outlier: 3.828A pdb=" N GLU F 299 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR F 300 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'F' and resid 328 through 351 removed outlier: 3.594A pdb=" N ILE F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Proline residue: F 338 - end of helix Processing helix chain 'F' and resid 360 through 379 removed outlier: 3.605A pdb=" N ARG F 370 " --> pdb=" O ILE F 366 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE F 375 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG F 379 " --> pdb=" O PHE F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 392 Processing helix chain 'F' and resid 395 through 420 Processing helix chain 'F' and resid 431 through 441 removed outlier: 3.571A pdb=" N PHE F 435 " --> pdb=" O ILE F 431 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 441 " --> pdb=" O TRP F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 removed outlier: 4.003A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 491 removed outlier: 4.176A pdb=" N GLU F 490 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 491 " --> pdb=" O TYR F 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 78 Processing helix chain 'G' and resid 90 through 106 removed outlier: 6.313A pdb=" N ALA G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 98 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 99 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 102 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE G 103 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 106 " --> pdb=" O ILE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 192 through 204 Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 229 through 235 Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 280 through 299 removed outlier: 3.972A pdb=" N ARG G 284 " --> pdb=" O GLU G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 309 Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.880A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA G 336 " --> pdb=" O GLU G 332 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE G 337 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN G 338 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Proline residue: G 341 - end of helix Processing helix chain 'G' and resid 345 through 355 Processing helix chain 'H' and resid 218 through 225 Processing helix chain 'H' and resid 231 through 255 removed outlier: 4.676A pdb=" N THR H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 315 removed outlier: 3.830A pdb=" N GLU H 299 " --> pdb=" O PHE H 296 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR H 300 " --> pdb=" O VAL H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'H' and resid 328 through 351 removed outlier: 3.595A pdb=" N ILE H 337 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Proline residue: H 338 - end of helix Processing helix chain 'H' and resid 360 through 379 removed outlier: 3.605A pdb=" N ARG H 370 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL H 371 " --> pdb=" O ARG H 367 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE H 372 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ARG H 373 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE H 374 " --> pdb=" O ARG H 370 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE H 375 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS H 376 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU H 377 " --> pdb=" O ARG H 373 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG H 379 " --> pdb=" O PHE H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 392 Processing helix chain 'H' and resid 395 through 420 Processing helix chain 'H' and resid 431 through 441 removed outlier: 3.571A pdb=" N PHE H 435 " --> pdb=" O ILE H 431 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP H 436 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR H 441 " --> pdb=" O TRP H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 473 removed outlier: 4.004A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 491 removed outlier: 4.175A pdb=" N GLU H 490 " --> pdb=" O PHE H 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR H 491 " --> pdb=" O TYR H 487 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 Processing helix chain 'I' and resid 90 through 106 removed outlier: 6.314A pdb=" N ALA I 95 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL I 98 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 99 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE I 102 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE I 103 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS I 106 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 112 No H-bonds generated for 'chain 'I' and resid 110 through 112' Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 133 through 146 Processing helix chain 'I' and resid 166 through 178 Processing helix chain 'I' and resid 192 through 204 Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 229 through 235 Processing helix chain 'I' and resid 247 through 249 No H-bonds generated for 'chain 'I' and resid 247 through 249' Processing helix chain 'I' and resid 271 through 277 Processing helix chain 'I' and resid 280 through 299 removed outlier: 3.973A pdb=" N ARG I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 309 Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.880A pdb=" N GLY I 335 " --> pdb=" O MET I 331 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA I 336 " --> pdb=" O GLU I 332 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE I 337 " --> pdb=" O ASN I 333 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN I 338 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL I 339 " --> pdb=" O GLY I 335 " (cutoff:3.500A) Proline residue: I 341 - end of helix Processing helix chain 'I' and resid 345 through 355 Processing helix chain 'J' and resid 119 through 124 removed outlier: 3.781A pdb=" N GLN J 124 " --> pdb=" O LYS J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 139 Processing helix chain 'J' and resid 156 through 164 removed outlier: 3.625A pdb=" N TYR J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 187 Processing helix chain 'J' and resid 192 through 200 Processing helix chain 'M' and resid 66 through 78 Processing helix chain 'M' and resid 90 through 106 removed outlier: 6.313A pdb=" N ALA M 95 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL M 98 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 99 " --> pdb=" O GLU M 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE M 102 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE M 103 " --> pdb=" O GLY M 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 106 " --> pdb=" O ILE M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 112 No H-bonds generated for 'chain 'M' and resid 110 through 112' Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 133 through 146 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 192 through 204 Processing helix chain 'M' and resid 223 through 227 Processing helix chain 'M' and resid 229 through 235 Processing helix chain 'M' and resid 247 through 249 No H-bonds generated for 'chain 'M' and resid 247 through 249' Processing helix chain 'M' and resid 271 through 277 Processing helix chain 'M' and resid 280 through 299 removed outlier: 3.972A pdb=" N ARG M 284 " --> pdb=" O GLU M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 303 through 309 Processing helix chain 'M' and resid 327 through 342 removed outlier: 3.879A pdb=" N GLY M 335 " --> pdb=" O MET M 331 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA M 336 " --> pdb=" O GLU M 332 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ILE M 337 " --> pdb=" O ASN M 333 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN M 338 " --> pdb=" O ILE M 334 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL M 339 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Proline residue: M 341 - end of helix Processing helix chain 'M' and resid 345 through 355 Processing helix chain 'N' and resid 119 through 124 removed outlier: 3.780A pdb=" N GLN N 124 " --> pdb=" O LYS N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 139 Processing helix chain 'N' and resid 156 through 164 removed outlier: 3.626A pdb=" N TYR N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 187 Processing helix chain 'N' and resid 192 through 200 Processing helix chain 'O' and resid 119 through 124 removed outlier: 3.781A pdb=" N GLN O 124 " --> pdb=" O LYS O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 139 Processing helix chain 'O' and resid 156 through 164 removed outlier: 3.626A pdb=" N TYR O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 187 Processing helix chain 'O' and resid 192 through 200 Processing helix chain 'P' and resid 119 through 124 removed outlier: 3.781A pdb=" N GLN P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 139 Processing helix chain 'P' and resid 156 through 164 removed outlier: 3.626A pdb=" N TYR P 163 " --> pdb=" O ILE P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 187 Processing helix chain 'P' and resid 192 through 200 Processing sheet with id= A, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'C' and resid 52 through 54 removed outlier: 7.971A pdb=" N GLY C 53 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 320 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 215 " --> pdb=" O MET C 241 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.347A pdb=" N VAL C 114 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 154 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 156 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR C 184 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA C 157 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY C 186 " --> pdb=" O ALA C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= E, first strand: chain 'G' and resid 52 through 54 removed outlier: 7.971A pdb=" N GLY G 53 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL G 320 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 215 " --> pdb=" O MET G 241 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 83 through 85 removed outlier: 6.348A pdb=" N VAL G 114 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL G 154 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE G 119 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE G 156 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA G 157 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY G 186 " --> pdb=" O ALA G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'I' and resid 39 through 41 Processing sheet with id= H, first strand: chain 'I' and resid 52 through 54 removed outlier: 7.971A pdb=" N GLY I 53 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL I 320 " --> pdb=" O GLY I 53 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA I 240 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL I 320 " --> pdb=" O ALA I 240 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR I 242 " --> pdb=" O VAL I 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU I 322 " --> pdb=" O THR I 242 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA I 215 " --> pdb=" O MET I 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.347A pdb=" N VAL I 114 " --> pdb=" O PHE I 84 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL I 154 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE I 119 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE I 156 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR I 184 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA I 157 " --> pdb=" O TYR I 184 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY I 186 " --> pdb=" O ALA I 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'J' and resid 113 through 118 removed outlier: 6.220A pdb=" N TYR J 147 " --> pdb=" O ASN J 109 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 39 through 41 Processing sheet with id= L, first strand: chain 'M' and resid 52 through 54 removed outlier: 7.972A pdb=" N GLY M 53 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL M 320 " --> pdb=" O GLY M 53 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA M 240 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL M 320 " --> pdb=" O ALA M 240 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR M 242 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU M 322 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 215 " --> pdb=" O MET M 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 83 through 85 removed outlier: 6.348A pdb=" N VAL M 114 " --> pdb=" O PHE M 84 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL M 154 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE M 119 " --> pdb=" O VAL M 154 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE M 156 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR M 184 " --> pdb=" O VAL M 155 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA M 157 " --> pdb=" O TYR M 184 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY M 186 " --> pdb=" O ALA M 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 113 through 118 removed outlier: 6.219A pdb=" N TYR N 147 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 113 through 118 removed outlier: 6.219A pdb=" N TYR O 147 " --> pdb=" O ASN O 109 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 113 through 118 removed outlier: 6.219A pdb=" N TYR P 147 " --> pdb=" O ASN P 109 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2448 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: 6.17 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3492 1.28 - 1.42: 5961 1.42 - 1.55: 12754 1.55 - 1.68: 97 1.68 - 1.81: 184 Bond restraints: 22488 Sorted by residual: bond pdb=" CA ILE B 337 " pdb=" CB ILE B 337 " ideal model delta sigma weight residual 1.534 1.433 0.101 6.80e-03 2.16e+04 2.22e+02 bond pdb=" CA ILE D 337 " pdb=" CB ILE D 337 " ideal model delta sigma weight residual 1.534 1.434 0.101 6.80e-03 2.16e+04 2.20e+02 bond pdb=" CA ILE H 337 " pdb=" CB ILE H 337 " ideal model delta sigma weight residual 1.534 1.434 0.100 6.80e-03 2.16e+04 2.17e+02 bond pdb=" CA ILE F 337 " pdb=" CB ILE F 337 " ideal model delta sigma weight residual 1.534 1.434 0.100 6.80e-03 2.16e+04 2.17e+02 bond pdb=" C ALA F 335 " pdb=" O ALA F 335 " ideal model delta sigma weight residual 1.236 1.397 -0.160 1.15e-02 7.56e+03 1.94e+02 ... (remaining 22483 not shown) Histogram of bond angle deviations from ideal: 83.03 - 93.61: 4 93.61 - 104.19: 382 104.19 - 114.78: 13341 114.78 - 125.36: 16285 125.36 - 135.94: 448 Bond angle restraints: 30460 Sorted by residual: angle pdb=" C ASP D 293 " pdb=" N PRO D 294 " pdb=" CA PRO D 294 " ideal model delta sigma weight residual 119.28 135.94 -16.66 1.10e+00 8.26e-01 2.29e+02 angle pdb=" C ASP B 293 " pdb=" N PRO B 294 " pdb=" CA PRO B 294 " ideal model delta sigma weight residual 119.28 135.93 -16.65 1.10e+00 8.26e-01 2.29e+02 angle pdb=" C ASP H 293 " pdb=" N PRO H 294 " pdb=" CA PRO H 294 " ideal model delta sigma weight residual 119.28 135.89 -16.61 1.10e+00 8.26e-01 2.28e+02 angle pdb=" C ASP F 293 " pdb=" N PRO F 294 " pdb=" CA PRO F 294 " ideal model delta sigma weight residual 119.28 135.86 -16.58 1.10e+00 8.26e-01 2.27e+02 angle pdb=" CA LEU B 347 " pdb=" CB LEU B 347 " pdb=" CG LEU B 347 " ideal model delta sigma weight residual 116.30 83.03 33.27 3.50e+00 8.16e-02 9.03e+01 ... (remaining 30455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 12038 17.00 - 34.00: 1027 34.00 - 51.01: 335 51.01 - 68.01: 96 68.01 - 85.01: 52 Dihedral angle restraints: 13548 sinusoidal: 5660 harmonic: 7888 Sorted by residual: dihedral pdb=" C PHE F 296 " pdb=" N PHE F 296 " pdb=" CA PHE F 296 " pdb=" CB PHE F 296 " ideal model delta harmonic sigma weight residual -122.60 -145.09 22.49 0 2.50e+00 1.60e-01 8.09e+01 dihedral pdb=" C PHE D 296 " pdb=" N PHE D 296 " pdb=" CA PHE D 296 " pdb=" CB PHE D 296 " ideal model delta harmonic sigma weight residual -122.60 -145.08 22.48 0 2.50e+00 1.60e-01 8.09e+01 dihedral pdb=" C PHE B 296 " pdb=" N PHE B 296 " pdb=" CA PHE B 296 " pdb=" CB PHE B 296 " ideal model delta harmonic sigma weight residual -122.60 -145.04 22.44 0 2.50e+00 1.60e-01 8.06e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3288 0.199 - 0.399: 57 0.399 - 0.598: 23 0.598 - 0.797: 8 0.797 - 0.996: 4 Chirality restraints: 3380 Sorted by residual: chirality pdb=" CA PHE D 296 " pdb=" N PHE D 296 " pdb=" C PHE D 296 " pdb=" CB PHE D 296 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA PHE F 296 " pdb=" N PHE F 296 " pdb=" C PHE F 296 " pdb=" CB PHE F 296 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA PHE B 296 " pdb=" N PHE B 296 " pdb=" C PHE B 296 " pdb=" CB PHE B 296 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 ... (remaining 3377 not shown) Planarity restraints: 3844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 338 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 337 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO F 338 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO F 338 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO F 338 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 337 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO H 338 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO H 338 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO H 338 " -0.055 5.00e-02 4.00e+02 ... (remaining 3841 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.69: 668 2.69 - 3.30: 23027 3.30 - 3.91: 40750 3.91 - 4.53: 56385 4.53 - 5.14: 87965 Nonbonded interactions: 208795 Sorted by model distance: nonbonded pdb=" OG1 THR B 300 " pdb=" OH TYR B 339 " model vdw 2.074 2.440 nonbonded pdb=" OG1 THR D 300 " pdb=" OH TYR D 339 " model vdw 2.074 2.440 nonbonded pdb=" OG1 THR H 300 " pdb=" OH TYR H 339 " model vdw 2.075 2.440 nonbonded pdb=" OG1 THR F 300 " pdb=" OH TYR F 339 " model vdw 2.076 2.440 nonbonded pdb=" OE2 GLU G 138 " pdb=" OH TYR M 151 " model vdw 2.307 2.440 ... (remaining 208790 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 'B' and resid 208 through 493) selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 16.530 Check model and map are aligned: 0.300 Set scattering table: 0.220 Process input model: 55.790 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.012 0.219 22488 Z= 0.754 Angle : 1.224 33.268 30460 Z= 0.710 Chirality : 0.091 0.996 3380 Planarity : 0.008 0.103 3844 Dihedral : 15.743 85.011 8464 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 7.69 % Allowed : 9.10 % Favored : 83.21 % Cbeta Deviations : 1.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 2704 helix: -0.32 (0.12), residues: 1516 sheet: 0.87 (0.39), residues: 172 loop : -2.41 (0.15), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 185 HIS 0.010 0.002 HIS M 135 PHE 0.039 0.003 PHE B 296 TYR 0.047 0.003 TYR B 339 ARG 0.004 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 426 time to evaluate : 2.678 Fit side-chains REVERT: B 242 LEU cc_start: 0.7272 (mt) cc_final: 0.7021 (mt) REVERT: B 296 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6292 (t80) REVERT: B 466 ILE cc_start: 0.7777 (mm) cc_final: 0.7559 (mt) REVERT: C 70 GLU cc_start: 0.7125 (tt0) cc_final: 0.6901 (tt0) REVERT: C 94 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7038 (mttp) REVERT: C 104 LYS cc_start: 0.7859 (tttp) cc_final: 0.7624 (ttmm) REVERT: C 105 LYS cc_start: 0.7841 (tttt) cc_final: 0.7613 (tttm) REVERT: C 129 ARG cc_start: 0.7343 (ptm160) cc_final: 0.7005 (ptt-90) REVERT: C 223 GLU cc_start: 0.7494 (tp30) cc_final: 0.7064 (tm-30) REVERT: C 290 LYS cc_start: 0.6517 (mtmt) cc_final: 0.6192 (mttm) REVERT: C 315 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6363 (mp0) REVERT: D 222 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5935 (mm) REVERT: D 242 LEU cc_start: 0.7276 (mt) cc_final: 0.7014 (mt) REVERT: D 296 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5752 (t80) REVERT: D 391 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (mp) REVERT: F 244 ILE cc_start: 0.6477 (mt) cc_final: 0.6128 (mt) REVERT: F 340 PHE cc_start: 0.8282 (m-10) cc_final: 0.8057 (m-80) REVERT: G 70 GLU cc_start: 0.6867 (tt0) cc_final: 0.6633 (tt0) REVERT: G 94 LYS cc_start: 0.7314 (mtpt) cc_final: 0.6923 (mttp) REVERT: G 124 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7500 (mmmm) REVERT: G 129 ARG cc_start: 0.7454 (ptm160) cc_final: 0.7027 (ptt-90) REVERT: G 223 GLU cc_start: 0.7558 (tp30) cc_final: 0.6960 (tm-30) REVERT: G 270 TYR cc_start: 0.7868 (m-80) cc_final: 0.7398 (m-80) REVERT: G 315 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6755 (mp0) REVERT: G 350 GLU cc_start: 0.7203 (tt0) cc_final: 0.6988 (tt0) REVERT: G 353 SER cc_start: 0.8002 (t) cc_final: 0.7758 (p) REVERT: H 222 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6065 (mm) REVERT: H 296 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6240 (t80) REVERT: H 386 ILE cc_start: 0.7984 (mt) cc_final: 0.7695 (mt) REVERT: I 70 GLU cc_start: 0.6918 (tt0) cc_final: 0.6464 (tt0) REVERT: I 94 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7079 (mttp) REVERT: I 104 LYS cc_start: 0.7773 (tttp) cc_final: 0.7507 (ttmm) REVERT: I 105 LYS cc_start: 0.7735 (tttt) cc_final: 0.7365 (tttt) REVERT: I 124 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7557 (mttp) REVERT: I 129 ARG cc_start: 0.7361 (ptm160) cc_final: 0.7035 (ptt-90) REVERT: I 223 GLU cc_start: 0.7552 (tp30) cc_final: 0.7252 (tm-30) REVERT: I 241 MET cc_start: 0.8768 (ttm) cc_final: 0.8543 (ttm) REVERT: I 290 LYS cc_start: 0.6740 (mtmt) cc_final: 0.6528 (mmtt) REVERT: I 315 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6532 (mp0) REVERT: J 104 GLU cc_start: 0.7428 (tt0) cc_final: 0.7181 (tt0) REVERT: J 170 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6744 (mtt-85) REVERT: M 70 GLU cc_start: 0.6884 (tt0) cc_final: 0.6674 (tt0) REVERT: M 94 LYS cc_start: 0.7330 (mtpt) cc_final: 0.6933 (mttp) REVERT: M 129 ARG cc_start: 0.7485 (ptm160) cc_final: 0.7220 (ptt-90) REVERT: M 223 GLU cc_start: 0.7625 (tp30) cc_final: 0.7099 (tm-30) REVERT: M 270 TYR cc_start: 0.7871 (m-80) cc_final: 0.7456 (m-80) REVERT: M 315 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6835 (mp0) REVERT: N 104 GLU cc_start: 0.7495 (tt0) cc_final: 0.7274 (tt0) REVERT: N 157 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: N 170 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6841 (mtt-85) REVERT: O 104 GLU cc_start: 0.7485 (tt0) cc_final: 0.7273 (tt0) REVERT: O 170 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6923 (mtt-85) REVERT: O 171 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7780 (ttp80) REVERT: P 104 GLU cc_start: 0.7492 (tt0) cc_final: 0.7220 (tt0) REVERT: P 135 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8078 (mtt180) REVERT: P 170 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6935 (mtt-85) outliers start: 180 outliers final: 77 residues processed: 561 average time/residue: 0.3810 time to fit residues: 313.9003 Evaluate side-chains 455 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 365 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 338 PRO Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 338 PRO Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 338 PRO Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain H residue 296 PHE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 338 PRO Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 349 GLU Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.0570 chunk 203 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN B 385 GLN C 293 GLN D 219 GLN I 293 GLN M 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22488 Z= 0.148 Angle : 0.505 5.580 30460 Z= 0.270 Chirality : 0.040 0.141 3380 Planarity : 0.005 0.038 3844 Dihedral : 12.000 87.032 3427 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.12 % Allowed : 10.98 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2704 helix: 0.60 (0.13), residues: 1544 sheet: 0.82 (0.35), residues: 216 loop : -2.03 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 243 HIS 0.004 0.001 HIS G 135 PHE 0.048 0.001 PHE D 216 TYR 0.017 0.001 TYR F 447 ARG 0.002 0.000 ARG F 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 366 time to evaluate : 2.226 Fit side-chains REVERT: B 242 LEU cc_start: 0.7103 (mt) cc_final: 0.6897 (mt) REVERT: C 94 LYS cc_start: 0.7447 (mtpt) cc_final: 0.6921 (mttp) REVERT: C 105 LYS cc_start: 0.7568 (tttt) cc_final: 0.7312 (tttm) REVERT: C 129 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6954 (ptt-90) REVERT: C 223 GLU cc_start: 0.7466 (tp30) cc_final: 0.6964 (tm-30) REVERT: C 290 LYS cc_start: 0.6467 (mtmt) cc_final: 0.6169 (mmtt) REVERT: C 315 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6644 (mm-30) REVERT: F 225 GLU cc_start: 0.4089 (mm-30) cc_final: 0.3817 (tp30) REVERT: F 244 ILE cc_start: 0.6577 (mt) cc_final: 0.6321 (mt) REVERT: G 70 GLU cc_start: 0.6782 (tt0) cc_final: 0.6561 (tt0) REVERT: G 94 LYS cc_start: 0.7311 (mtpt) cc_final: 0.6877 (mttp) REVERT: G 129 ARG cc_start: 0.7361 (ptm160) cc_final: 0.7010 (ptt-90) REVERT: G 223 GLU cc_start: 0.7481 (tp30) cc_final: 0.7245 (tm-30) REVERT: G 270 TYR cc_start: 0.7797 (m-80) cc_final: 0.7396 (m-80) REVERT: G 315 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6772 (mp0) REVERT: G 350 GLU cc_start: 0.7001 (tt0) cc_final: 0.6777 (tt0) REVERT: H 376 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6905 (mtpp) REVERT: H 386 ILE cc_start: 0.7926 (mt) cc_final: 0.7717 (mt) REVERT: I 94 LYS cc_start: 0.7379 (mtpt) cc_final: 0.6929 (mttp) REVERT: I 105 LYS cc_start: 0.7278 (tttt) cc_final: 0.7046 (tttm) REVERT: I 129 ARG cc_start: 0.7292 (ptm160) cc_final: 0.6962 (ptt-90) REVERT: J 170 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6795 (mtt-85) REVERT: M 70 GLU cc_start: 0.6775 (tt0) cc_final: 0.6360 (tt0) REVERT: M 94 LYS cc_start: 0.7341 (mtpt) cc_final: 0.6896 (mttp) REVERT: M 105 LYS cc_start: 0.7279 (tttt) cc_final: 0.6889 (tttm) REVERT: M 129 ARG cc_start: 0.7411 (ptm160) cc_final: 0.7085 (ptt-90) REVERT: M 223 GLU cc_start: 0.7510 (tp30) cc_final: 0.6999 (tm-30) REVERT: M 270 TYR cc_start: 0.7804 (m-80) cc_final: 0.7396 (m-80) REVERT: M 315 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6843 (mp0) REVERT: N 170 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6869 (mtt-85) REVERT: N 194 MET cc_start: 0.7507 (mmt) cc_final: 0.7307 (mmt) REVERT: O 168 ARG cc_start: 0.7802 (mtm180) cc_final: 0.7375 (mtm-85) REVERT: O 170 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6974 (mmt-90) REVERT: P 135 ARG cc_start: 0.8473 (mtt180) cc_final: 0.8017 (mtt180) REVERT: P 170 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6960 (mtt-85) REVERT: P 171 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7856 (ttp80) outliers start: 73 outliers final: 46 residues processed: 417 average time/residue: 0.3806 time to fit residues: 232.6474 Evaluate side-chains 398 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 348 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 0.0770 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 263 optimal weight: 0.5980 chunk 217 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN D 219 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22488 Z= 0.142 Angle : 0.476 5.327 30460 Z= 0.248 Chirality : 0.040 0.148 3380 Planarity : 0.004 0.039 3844 Dihedral : 9.303 89.031 3337 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 11.75 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2704 helix: 1.17 (0.14), residues: 1556 sheet: 0.16 (0.39), residues: 152 loop : -1.55 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 185 HIS 0.008 0.001 HIS F 451 PHE 0.027 0.001 PHE D 216 TYR 0.013 0.001 TYR F 447 ARG 0.001 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 358 time to evaluate : 2.336 Fit side-chains REVERT: C 94 LYS cc_start: 0.7532 (mtpt) cc_final: 0.6970 (mttp) REVERT: C 105 LYS cc_start: 0.7509 (tttt) cc_final: 0.7171 (tttm) REVERT: C 129 ARG cc_start: 0.7217 (ptm160) cc_final: 0.6896 (ptt-90) REVERT: C 223 GLU cc_start: 0.7486 (tp30) cc_final: 0.6959 (tm-30) REVERT: C 290 LYS cc_start: 0.6451 (mtmt) cc_final: 0.6165 (mmtt) REVERT: F 303 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6547 (mp) REVERT: G 51 CYS cc_start: 0.6368 (m) cc_final: 0.6037 (m) REVERT: G 94 LYS cc_start: 0.7212 (mtpt) cc_final: 0.6795 (mttp) REVERT: G 129 ARG cc_start: 0.7266 (ptm160) cc_final: 0.6953 (ptt-90) REVERT: G 223 GLU cc_start: 0.7524 (tp30) cc_final: 0.7285 (tm-30) REVERT: G 270 TYR cc_start: 0.7667 (m-80) cc_final: 0.7250 (m-80) REVERT: G 315 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6741 (mp0) REVERT: I 94 LYS cc_start: 0.7416 (mtpt) cc_final: 0.6879 (mttp) REVERT: I 105 LYS cc_start: 0.7312 (tttt) cc_final: 0.7084 (tttm) REVERT: I 129 ARG cc_start: 0.7228 (ptm160) cc_final: 0.6909 (ptt-90) REVERT: J 170 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6760 (mtt-85) REVERT: M 51 CYS cc_start: 0.6412 (m) cc_final: 0.6099 (m) REVERT: M 70 GLU cc_start: 0.6857 (tt0) cc_final: 0.6442 (tt0) REVERT: M 94 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6813 (mttp) REVERT: M 105 LYS cc_start: 0.7312 (tttt) cc_final: 0.6976 (tttm) REVERT: M 129 ARG cc_start: 0.7318 (ptm160) cc_final: 0.7013 (ptt-90) REVERT: M 223 GLU cc_start: 0.7518 (tp30) cc_final: 0.7263 (tm-30) REVERT: M 270 TYR cc_start: 0.7691 (m-80) cc_final: 0.7273 (m-80) REVERT: M 289 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5911 (mp) REVERT: M 315 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6730 (mp0) REVERT: N 170 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6891 (mmt-90) REVERT: O 170 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6906 (mmt-90) REVERT: P 135 ARG cc_start: 0.8492 (mtt180) cc_final: 0.8053 (mtt180) REVERT: P 170 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6857 (mtt-85) outliers start: 57 outliers final: 35 residues processed: 400 average time/residue: 0.3972 time to fit residues: 231.7285 Evaluate side-chains 390 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 349 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 0.0670 chunk 163 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN F 219 GLN G 293 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22488 Z= 0.281 Angle : 0.569 5.854 30460 Z= 0.299 Chirality : 0.044 0.158 3380 Planarity : 0.005 0.041 3844 Dihedral : 11.071 86.941 3314 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 3.59 % Allowed : 11.92 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2704 helix: 1.06 (0.14), residues: 1552 sheet: 0.69 (0.35), residues: 212 loop : -1.80 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 185 HIS 0.006 0.001 HIS G 135 PHE 0.018 0.001 PHE M 60 TYR 0.014 0.002 TYR F 487 ARG 0.004 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 343 time to evaluate : 2.491 Fit side-chains REVERT: C 94 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7120 (mttp) REVERT: C 105 LYS cc_start: 0.7701 (tttt) cc_final: 0.7431 (tttm) REVERT: C 129 ARG cc_start: 0.7413 (ptm160) cc_final: 0.7112 (ptt-90) REVERT: C 223 GLU cc_start: 0.7594 (tp30) cc_final: 0.7012 (tm-30) REVERT: C 290 LYS cc_start: 0.6415 (mtmt) cc_final: 0.6192 (mmtt) REVERT: G 94 LYS cc_start: 0.7413 (mtpt) cc_final: 0.7039 (mttp) REVERT: G 105 LYS cc_start: 0.7420 (tttt) cc_final: 0.7111 (tttm) REVERT: G 129 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7219 (ptt-90) REVERT: G 223 GLU cc_start: 0.7561 (tp30) cc_final: 0.7339 (tm-30) REVERT: I 94 LYS cc_start: 0.7503 (mtpt) cc_final: 0.7029 (mttp) REVERT: I 105 LYS cc_start: 0.7476 (tttt) cc_final: 0.7223 (tttm) REVERT: I 129 ARG cc_start: 0.7413 (ptm160) cc_final: 0.7096 (ptt-90) REVERT: J 170 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6771 (mtt-85) REVERT: M 70 GLU cc_start: 0.6935 (tt0) cc_final: 0.6508 (tt0) REVERT: M 94 LYS cc_start: 0.7422 (mtpt) cc_final: 0.7060 (mttp) REVERT: M 105 LYS cc_start: 0.7417 (tttt) cc_final: 0.7081 (tttm) REVERT: M 129 ARG cc_start: 0.7489 (ptm160) cc_final: 0.7142 (ptt-90) REVERT: M 223 GLU cc_start: 0.7582 (tp30) cc_final: 0.7367 (tm-30) REVERT: N 170 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6828 (mtt-85) REVERT: O 170 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6894 (mmt-90) REVERT: P 170 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6914 (mtt-85) outliers start: 84 outliers final: 61 residues processed: 407 average time/residue: 0.3992 time to fit residues: 239.4336 Evaluate side-chains 393 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 328 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 353 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 22488 Z= 0.529 Angle : 0.715 8.054 30460 Z= 0.377 Chirality : 0.052 0.237 3380 Planarity : 0.006 0.045 3844 Dihedral : 11.401 83.947 3314 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.29 % Favored : 95.45 % Rotamer: Outliers : 4.23 % Allowed : 12.01 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2704 helix: 0.59 (0.13), residues: 1552 sheet: 0.73 (0.39), residues: 172 loop : -1.91 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 57 HIS 0.007 0.002 HIS G 135 PHE 0.027 0.002 PHE M 60 TYR 0.024 0.003 TYR B 485 ARG 0.004 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 332 time to evaluate : 2.668 Fit side-chains REVERT: C 94 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7135 (mttp) REVERT: C 105 LYS cc_start: 0.7704 (tttt) cc_final: 0.7446 (tttm) REVERT: C 129 ARG cc_start: 0.7431 (ptm160) cc_final: 0.7168 (ptt-90) REVERT: C 223 GLU cc_start: 0.7661 (tp30) cc_final: 0.7056 (tm-30) REVERT: F 222 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6101 (mm) REVERT: G 94 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7055 (mttp) REVERT: G 105 LYS cc_start: 0.7470 (tttt) cc_final: 0.7151 (tttm) REVERT: G 129 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7279 (ptt-90) REVERT: G 223 GLU cc_start: 0.7586 (tp30) cc_final: 0.7358 (tm-30) REVERT: G 297 GLU cc_start: 0.7041 (tt0) cc_final: 0.6827 (mt-10) REVERT: H 485 TYR cc_start: 0.6510 (t80) cc_final: 0.6286 (t80) REVERT: I 94 LYS cc_start: 0.7462 (mtpt) cc_final: 0.7064 (mttp) REVERT: I 105 LYS cc_start: 0.7585 (tttt) cc_final: 0.7245 (tttm) REVERT: I 129 ARG cc_start: 0.7456 (ptm160) cc_final: 0.7187 (ptt-90) REVERT: J 135 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8317 (mtt180) REVERT: J 170 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6834 (mtt-85) REVERT: M 70 GLU cc_start: 0.6975 (tt0) cc_final: 0.6551 (tt0) REVERT: M 94 LYS cc_start: 0.7446 (mtpt) cc_final: 0.7065 (mttp) REVERT: M 105 LYS cc_start: 0.7494 (tttt) cc_final: 0.7130 (tttm) REVERT: M 129 ARG cc_start: 0.7545 (ptm160) cc_final: 0.7242 (ptt-90) REVERT: M 223 GLU cc_start: 0.7601 (tp30) cc_final: 0.7374 (tm-30) REVERT: N 170 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6874 (mtt-85) REVERT: O 170 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6948 (mtt-85) REVERT: P 170 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6864 (mtt-85) outliers start: 99 outliers final: 80 residues processed: 405 average time/residue: 0.3895 time to fit residues: 230.8048 Evaluate side-chains 409 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 324 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 347 ILE Chi-restraints excluded: chain M residue 353 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Chi-restraints excluded: chain P residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 152 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 259 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN D 219 GLN F 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22488 Z= 0.144 Angle : 0.475 5.339 30460 Z= 0.251 Chirality : 0.040 0.135 3380 Planarity : 0.004 0.041 3844 Dihedral : 9.516 85.537 3313 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.81 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 14.02 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2704 helix: 1.28 (0.14), residues: 1540 sheet: 0.34 (0.42), residues: 132 loop : -1.64 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 185 HIS 0.005 0.001 HIS G 135 PHE 0.026 0.001 PHE D 314 TYR 0.021 0.001 TYR B 485 ARG 0.002 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 342 time to evaluate : 2.857 Fit side-chains REVERT: C 94 LYS cc_start: 0.7425 (mtpt) cc_final: 0.6987 (mttp) REVERT: C 105 LYS cc_start: 0.7667 (tttt) cc_final: 0.7412 (tttm) REVERT: C 129 ARG cc_start: 0.7223 (ptm160) cc_final: 0.6896 (ptt-90) REVERT: C 223 GLU cc_start: 0.7611 (tp30) cc_final: 0.7029 (tm-30) REVERT: F 222 LEU cc_start: 0.6553 (tp) cc_final: 0.6167 (mm) REVERT: F 242 LEU cc_start: 0.6770 (mt) cc_final: 0.6549 (mt) REVERT: F 485 TYR cc_start: 0.6642 (t80) cc_final: 0.6358 (t80) REVERT: G 94 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6960 (mttp) REVERT: G 105 LYS cc_start: 0.7392 (tttt) cc_final: 0.7099 (tttm) REVERT: G 129 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6969 (ptt-90) REVERT: H 485 TYR cc_start: 0.6522 (t80) cc_final: 0.6273 (t80) REVERT: I 94 LYS cc_start: 0.7397 (mtpt) cc_final: 0.6987 (mttp) REVERT: I 105 LYS cc_start: 0.7526 (tttt) cc_final: 0.7270 (tttm) REVERT: I 129 ARG cc_start: 0.7218 (ptm160) cc_final: 0.6899 (ptt-90) REVERT: J 170 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6703 (mtt-85) REVERT: M 40 ARG cc_start: 0.7721 (ptp-170) cc_final: 0.7235 (ptp-170) REVERT: M 70 GLU cc_start: 0.6871 (tt0) cc_final: 0.6401 (tt0) REVERT: M 94 LYS cc_start: 0.7387 (mtpt) cc_final: 0.6968 (mttp) REVERT: M 105 LYS cc_start: 0.7392 (tttt) cc_final: 0.7044 (tttm) REVERT: M 129 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6954 (ptt-90) REVERT: N 170 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6730 (mmt-90) REVERT: O 170 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6861 (mmt-90) REVERT: P 170 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6798 (mmt-90) outliers start: 62 outliers final: 43 residues processed: 389 average time/residue: 0.3985 time to fit residues: 225.2273 Evaluate side-chains 378 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 331 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 146 optimal weight: 0.3980 chunk 218 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN D 219 GLN G 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22488 Z= 0.176 Angle : 0.493 7.631 30460 Z= 0.259 Chirality : 0.040 0.143 3380 Planarity : 0.004 0.041 3844 Dihedral : 9.440 85.218 3313 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.70 % Favored : 97.00 % Rotamer: Outliers : 2.56 % Allowed : 13.93 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2704 helix: 1.39 (0.14), residues: 1544 sheet: 0.05 (0.40), residues: 148 loop : -1.55 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.006 0.001 HIS M 135 PHE 0.016 0.001 PHE D 406 TYR 0.022 0.001 TYR B 485 ARG 0.003 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 340 time to evaluate : 2.739 Fit side-chains REVERT: C 94 LYS cc_start: 0.7446 (mtpt) cc_final: 0.7001 (mttp) REVERT: C 105 LYS cc_start: 0.7648 (tttt) cc_final: 0.7386 (tttm) REVERT: C 129 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6986 (ptt-90) REVERT: C 223 GLU cc_start: 0.7603 (tp30) cc_final: 0.7027 (tm-30) REVERT: F 222 LEU cc_start: 0.6588 (tp) cc_final: 0.6204 (mm) REVERT: F 242 LEU cc_start: 0.6813 (mt) cc_final: 0.6585 (mt) REVERT: F 485 TYR cc_start: 0.6647 (t80) cc_final: 0.6354 (t80) REVERT: G 70 GLU cc_start: 0.7259 (tt0) cc_final: 0.6856 (tt0) REVERT: G 94 LYS cc_start: 0.7389 (mtpt) cc_final: 0.6956 (mttp) REVERT: G 105 LYS cc_start: 0.7387 (tttt) cc_final: 0.7034 (tttm) REVERT: G 129 ARG cc_start: 0.7379 (ptm160) cc_final: 0.7026 (ptt-90) REVERT: H 485 TYR cc_start: 0.6561 (t80) cc_final: 0.6321 (t80) REVERT: I 94 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6987 (mttp) REVERT: I 105 LYS cc_start: 0.7512 (tttt) cc_final: 0.7253 (tttm) REVERT: I 129 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6971 (ptt-90) REVERT: J 170 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6713 (mmt-90) REVERT: M 70 GLU cc_start: 0.6950 (tt0) cc_final: 0.6514 (tt0) REVERT: M 94 LYS cc_start: 0.7392 (mtpt) cc_final: 0.6970 (mttp) REVERT: M 105 LYS cc_start: 0.7399 (tttt) cc_final: 0.7048 (tttm) REVERT: M 129 ARG cc_start: 0.7351 (ptm160) cc_final: 0.7033 (ptt-90) REVERT: N 170 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6788 (mmt-90) REVERT: O 105 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7006 (mtm180) REVERT: O 170 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6934 (mmt-90) REVERT: P 170 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6815 (mmt-90) outliers start: 60 outliers final: 53 residues processed: 383 average time/residue: 0.4025 time to fit residues: 224.4188 Evaluate side-chains 393 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 335 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 223 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 0.0170 chunk 127 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN G 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22488 Z= 0.242 Angle : 0.535 7.297 30460 Z= 0.281 Chirality : 0.042 0.143 3380 Planarity : 0.005 0.041 3844 Dihedral : 9.962 84.215 3313 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.25 % Favored : 96.45 % Rotamer: Outliers : 2.99 % Allowed : 13.76 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2704 helix: 1.28 (0.14), residues: 1548 sheet: -0.05 (0.39), residues: 148 loop : -1.58 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 185 HIS 0.006 0.001 HIS G 135 PHE 0.021 0.001 PHE B 314 TYR 0.025 0.002 TYR B 485 ARG 0.004 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 339 time to evaluate : 2.550 Fit side-chains REVERT: C 94 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7016 (mttp) REVERT: C 105 LYS cc_start: 0.7661 (tttt) cc_final: 0.7402 (tttm) REVERT: C 129 ARG cc_start: 0.7376 (ptm160) cc_final: 0.7095 (ptt-90) REVERT: F 222 LEU cc_start: 0.6596 (tp) cc_final: 0.6207 (mm) REVERT: F 242 LEU cc_start: 0.6835 (mt) cc_final: 0.6607 (mt) REVERT: F 485 TYR cc_start: 0.6628 (t80) cc_final: 0.6352 (t80) REVERT: G 94 LYS cc_start: 0.7405 (mtpt) cc_final: 0.6974 (mttp) REVERT: G 105 LYS cc_start: 0.7397 (tttt) cc_final: 0.7078 (tttm) REVERT: G 129 ARG cc_start: 0.7457 (ptm160) cc_final: 0.7115 (ptt-90) REVERT: G 256 ASP cc_start: 0.8301 (p0) cc_final: 0.8097 (p0) REVERT: I 94 LYS cc_start: 0.7421 (mtpt) cc_final: 0.7002 (mttp) REVERT: I 105 LYS cc_start: 0.7519 (tttt) cc_final: 0.7262 (tttm) REVERT: I 129 ARG cc_start: 0.7347 (ptm160) cc_final: 0.6975 (ptt-90) REVERT: J 170 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6784 (mmt-90) REVERT: M 94 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6991 (mttp) REVERT: M 105 LYS cc_start: 0.7412 (tttt) cc_final: 0.7087 (tttm) REVERT: M 129 ARG cc_start: 0.7433 (ptm160) cc_final: 0.7100 (ptt-90) REVERT: N 170 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6808 (mmt-90) REVERT: O 105 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7020 (mtm180) REVERT: O 170 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6965 (mmt-90) REVERT: P 170 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6836 (mmt-90) outliers start: 70 outliers final: 61 residues processed: 389 average time/residue: 0.3867 time to fit residues: 219.2488 Evaluate side-chains 402 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 336 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 223 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Chi-restraints excluded: chain P residue 178 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 0.0060 chunk 225 optimal weight: 0.0970 chunk 240 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22488 Z= 0.138 Angle : 0.468 8.089 30460 Z= 0.245 Chirality : 0.039 0.125 3380 Planarity : 0.004 0.041 3844 Dihedral : 8.904 84.153 3313 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.00 % Favored : 97.86 % Rotamer: Outliers : 2.52 % Allowed : 14.15 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2704 helix: 1.53 (0.14), residues: 1544 sheet: 0.38 (0.44), residues: 128 loop : -1.51 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 185 HIS 0.004 0.001 HIS G 135 PHE 0.019 0.001 PHE B 314 TYR 0.025 0.001 TYR B 485 ARG 0.003 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 348 time to evaluate : 2.497 Fit side-chains REVERT: C 40 ARG cc_start: 0.7576 (ptp-170) cc_final: 0.7365 (ptp-170) REVERT: C 94 LYS cc_start: 0.7372 (mtpt) cc_final: 0.6904 (mttp) REVERT: C 105 LYS cc_start: 0.7558 (tttt) cc_final: 0.7294 (tttm) REVERT: C 129 ARG cc_start: 0.7200 (ptm160) cc_final: 0.6892 (ptt-90) REVERT: C 223 GLU cc_start: 0.7620 (tp30) cc_final: 0.7337 (tm-30) REVERT: D 315 PHE cc_start: 0.4225 (m-10) cc_final: 0.3982 (m-10) REVERT: F 222 LEU cc_start: 0.6520 (tp) cc_final: 0.6193 (mm) REVERT: F 242 LEU cc_start: 0.6876 (mt) cc_final: 0.6655 (mt) REVERT: G 94 LYS cc_start: 0.7307 (mtpt) cc_final: 0.6834 (mttp) REVERT: G 105 LYS cc_start: 0.7286 (tttt) cc_final: 0.6976 (tttm) REVERT: G 129 ARG cc_start: 0.7318 (ptm160) cc_final: 0.6963 (ptt-90) REVERT: I 94 LYS cc_start: 0.7356 (mtpt) cc_final: 0.6918 (mttp) REVERT: I 105 LYS cc_start: 0.7512 (tttt) cc_final: 0.7255 (tttm) REVERT: I 129 ARG cc_start: 0.7207 (ptm160) cc_final: 0.6881 (ptt-90) REVERT: J 170 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6762 (mmt-90) REVERT: M 94 LYS cc_start: 0.7365 (mtpt) cc_final: 0.6910 (mttp) REVERT: M 105 LYS cc_start: 0.7313 (tttt) cc_final: 0.7056 (tttm) REVERT: M 129 ARG cc_start: 0.7275 (ptm160) cc_final: 0.6954 (ptt-90) REVERT: M 289 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5975 (mp) REVERT: N 170 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6762 (mmt-90) REVERT: O 105 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.6970 (mtm180) REVERT: O 170 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6953 (mmt-90) REVERT: P 170 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6809 (mmt-90) outliers start: 59 outliers final: 45 residues processed: 394 average time/residue: 0.4062 time to fit residues: 232.0690 Evaluate side-chains 394 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 212 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN C 293 GLN G 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22488 Z= 0.178 Angle : 0.491 5.321 30460 Z= 0.257 Chirality : 0.040 0.125 3380 Planarity : 0.004 0.042 3844 Dihedral : 9.032 83.320 3307 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.77 % Favored : 96.93 % Rotamer: Outliers : 2.35 % Allowed : 14.10 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2704 helix: 1.49 (0.14), residues: 1548 sheet: 0.09 (0.39), residues: 148 loop : -1.46 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 185 HIS 0.005 0.001 HIS M 135 PHE 0.018 0.001 PHE B 314 TYR 0.027 0.001 TYR B 485 ARG 0.003 0.000 ARG C 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 343 time to evaluate : 2.636 Fit side-chains REVERT: C 40 ARG cc_start: 0.7750 (ptp-170) cc_final: 0.7390 (ptp-170) REVERT: C 94 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6979 (mttp) REVERT: C 105 LYS cc_start: 0.7632 (tttt) cc_final: 0.7375 (tttm) REVERT: C 129 ARG cc_start: 0.7275 (ptm160) cc_final: 0.6984 (ptt-90) REVERT: C 223 GLU cc_start: 0.7616 (tp30) cc_final: 0.7302 (tm-30) REVERT: D 315 PHE cc_start: 0.4207 (m-10) cc_final: 0.3978 (m-10) REVERT: F 222 LEU cc_start: 0.6555 (tp) cc_final: 0.6222 (mm) REVERT: F 242 LEU cc_start: 0.6868 (mt) cc_final: 0.6654 (mt) REVERT: F 485 TYR cc_start: 0.6652 (t80) cc_final: 0.6360 (t80) REVERT: G 94 LYS cc_start: 0.7350 (mtpt) cc_final: 0.6887 (mttp) REVERT: G 105 LYS cc_start: 0.7330 (tttt) cc_final: 0.7035 (tttm) REVERT: G 129 ARG cc_start: 0.7400 (ptm160) cc_final: 0.7044 (ptt-90) REVERT: I 94 LYS cc_start: 0.7411 (mtpt) cc_final: 0.6972 (mttp) REVERT: I 105 LYS cc_start: 0.7509 (tttt) cc_final: 0.7249 (tttm) REVERT: I 129 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6913 (ptt-90) REVERT: J 170 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6769 (mmt-90) REVERT: M 94 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6962 (mttp) REVERT: M 105 LYS cc_start: 0.7340 (tttt) cc_final: 0.7080 (tttm) REVERT: M 129 ARG cc_start: 0.7358 (ptm160) cc_final: 0.7037 (ptt-90) REVERT: N 170 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6779 (mmt-90) REVERT: O 105 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7002 (mtm180) REVERT: O 170 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6991 (mmt-90) REVERT: P 170 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6833 (mmt-90) outliers start: 55 outliers final: 45 residues processed: 386 average time/residue: 0.3919 time to fit residues: 220.0896 Evaluate side-chains 393 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 343 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 GLN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain I residue 223 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 181 SER Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 178 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 212 optimal weight: 0.0370 chunk 89 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 186 optimal weight: 0.3980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN C 293 GLN G 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.133897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.100088 restraints weight = 25076.592| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.21 r_work: 0.2485 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22488 Z= 0.131 Angle : 0.452 5.092 30460 Z= 0.236 Chirality : 0.039 0.119 3380 Planarity : 0.004 0.041 3844 Dihedral : 8.102 82.653 3303 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 2.09 % Allowed : 14.44 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2704 helix: 1.67 (0.14), residues: 1548 sheet: 0.66 (0.43), residues: 132 loop : -1.43 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 185 HIS 0.004 0.001 HIS C 135 PHE 0.016 0.001 PHE B 314 TYR 0.027 0.001 TYR B 485 ARG 0.003 0.000 ARG I 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.27 seconds wall clock time: 91 minutes 54.33 seconds (5514.33 seconds total)