Starting phenix.real_space_refine (version: dev) on Fri Feb 24 05:14:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2023/7wf3_32459_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2023/7wf3_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_2023/7wf3_32459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2023/7wf3_32459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2023/7wf3_32459_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wf3_32459/02_2023/7wf3_32459_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.041 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.37, per 1000 atoms: 0.56 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: 8.24 Conformation dependent library (CDL) restraints added in 3.1 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: 1.85 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: 6.34 Time building geometry restraints manager: 8.93 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: 11978 17.00 - 34.00: 958 34.00 - 51.01: 320 51.01 - 68.01: 72 68.01 - 85.01: 36 Dihedral angle restraints: 13364 sinusoidal: 5476 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 13361 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 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. 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: 3.870 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: 0.020 Extract box with map and model: 18.050 Check model and map are aligned: 0.400 Process input model: 54.790 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 14.952 85.011 8280 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 % 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 *********************** 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 : 2.828 Fit side-chains outliers start: 180 outliers final: 77 residues processed: 561 average time/residue: 0.3982 time to fit residues: 329.1441 Evaluate side-chains 429 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 352 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 4 residues processed: 77 average time/residue: 0.1912 time to fit residues: 31.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.1701 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= 0.153 Angle : 0.509 5.379 30460 Z= 0.274 Chirality : 0.040 0.145 3380 Planarity : 0.005 0.048 3844 Dihedral : 6.337 55.399 3084 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.58 % 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: -0.42 (0.15), residues: 2704 helix: 0.63 (0.13), residues: 1544 sheet: 0.39 (0.38), residues: 176 loop : -1.86 (0.17), residues: 984 *********************** 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 395 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 358 time to evaluate : 2.630 Fit side-chains outliers start: 37 outliers final: 20 residues processed: 378 average time/residue: 0.3822 time to fit residues: 214.0728 Evaluate side-chains 359 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 339 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2017 time to fit residues: 10.8096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 263 optimal weight: 0.0770 chunk 217 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 D 219 GLN M 293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2082 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= 0.139 Angle : 0.464 5.167 30460 Z= 0.246 Chirality : 0.039 0.145 3380 Planarity : 0.004 0.039 3844 Dihedral : 5.453 53.634 3084 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.28 % 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: 0.16 (0.16), residues: 2704 helix: 1.15 (0.14), residues: 1548 sheet: 0.24 (0.39), residues: 152 loop : -1.59 (0.17), residues: 1004 *********************** 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 377 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 347 time to evaluate : 2.540 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 367 average time/residue: 0.4221 time to fit residues: 227.8293 Evaluate side-chains 353 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 336 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2359 time to fit residues: 10.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 163 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN 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: 0.7721 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 22488 Z= 0.306 Angle : 0.584 6.261 30460 Z= 0.309 Chirality : 0.045 0.162 3380 Planarity : 0.005 0.042 3844 Dihedral : 6.631 57.768 3084 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.44 % Favored : 96.38 % Rotamer Outliers : 1.62 % 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: -0.01 (0.16), residues: 2704 helix: 0.96 (0.14), residues: 1552 sheet: 0.67 (0.35), residues: 212 loop : -1.83 (0.18), residues: 940 *********************** 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 373 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 335 time to evaluate : 2.719 Fit side-chains outliers start: 38 outliers final: 16 residues processed: 360 average time/residue: 0.3888 time to fit residues: 207.9864 Evaluate side-chains 334 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 318 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1982 time to fit residues: 9.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 3 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 22488 Z= 0.142 Angle : 0.455 5.277 30460 Z= 0.243 Chirality : 0.039 0.129 3380 Planarity : 0.004 0.040 3844 Dihedral : 5.672 59.875 3084 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.19 % Rotamer Outliers : 0.98 % 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: 0.40 (0.16), residues: 2704 helix: 1.35 (0.14), residues: 1548 sheet: 0.22 (0.39), residues: 152 loop : -1.48 (0.18), residues: 1004 *********************** 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 358 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 335 time to evaluate : 2.637 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 356 average time/residue: 0.4061 time to fit residues: 213.9340 Evaluate side-chains 340 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 323 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1961 time to fit residues: 9.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 0.0570 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2696 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= 0.149 Angle : 0.460 5.340 30460 Z= 0.244 Chirality : 0.039 0.122 3380 Planarity : 0.004 0.040 3844 Dihedral : 5.543 59.899 3084 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Rotamer Outliers : 0.64 % 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: 0.56 (0.16), residues: 2704 helix: 1.49 (0.14), residues: 1548 sheet: 0.13 (0.40), residues: 148 loop : -1.41 (0.18), residues: 1008 *********************** 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 350 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 335 time to evaluate : 2.098 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 343 average time/residue: 0.4076 time to fit residues: 205.4199 Evaluate side-chains 334 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 325 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2056 time to fit residues: 7.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22488 Z= 0.163 Angle : 0.467 5.321 30460 Z= 0.247 Chirality : 0.040 0.122 3380 Planarity : 0.004 0.041 3844 Dihedral : 5.554 59.884 3084 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.48 % Favored : 97.41 % Rotamer Outliers : 0.43 % 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: 0.58 (0.16), residues: 2704 helix: 1.49 (0.14), residues: 1552 sheet: 0.13 (0.39), residues: 148 loop : -1.38 (0.18), residues: 1004 *********************** 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 341 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 331 time to evaluate : 2.527 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 337 average time/residue: 0.4202 time to fit residues: 208.9518 Evaluate side-chains 330 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 325 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2877 time to fit residues: 5.9976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 154 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 127 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN G 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 22488 Z= 0.167 Angle : 0.471 5.291 30460 Z= 0.249 Chirality : 0.040 0.121 3380 Planarity : 0.004 0.041 3844 Dihedral : 5.559 59.201 3084 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.00 % Rotamer Outliers : 0.34 % 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: 0.58 (0.16), residues: 2704 helix: 1.51 (0.14), residues: 1548 sheet: 0.12 (0.40), residues: 148 loop : -1.39 (0.18), residues: 1008 *********************** 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 340 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 332 time to evaluate : 2.689 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 338 average time/residue: 0.4071 time to fit residues: 202.6406 Evaluate side-chains 331 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 325 time to evaluate : 2.504 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1958 time to fit residues: 5.9611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 240 optimal weight: 0.1980 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 0.3980 chunk 227 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 G 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 22488 Z= 0.137 Angle : 0.449 5.225 30460 Z= 0.238 Chirality : 0.039 0.119 3380 Planarity : 0.004 0.041 3844 Dihedral : 5.330 59.933 3084 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.89 % Rotamer Outliers : 0.09 % 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: 0.71 (0.17), residues: 2704 helix: 1.59 (0.14), residues: 1552 sheet: 0.28 (0.39), residues: 152 loop : -1.34 (0.18), residues: 1000 *********************** 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 332 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 330 time to evaluate : 2.607 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 332 average time/residue: 0.4089 time to fit residues: 198.3640 Evaluate side-chains 325 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 324 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1874 time to fit residues: 3.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 0.0270 chunk 176 optimal weight: 0.4980 chunk 266 optimal weight: 2.9990 chunk 245 optimal weight: 0.0020 chunk 212 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.4846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 GLN F 451 HIS G 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 22488 Z= 0.131 Angle : 0.448 5.155 30460 Z= 0.236 Chirality : 0.039 0.119 3380 Planarity : 0.004 0.041 3844 Dihedral : 5.255 59.971 3084 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer Outliers : 0.17 % 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: 0.79 (0.17), residues: 2704 helix: 1.65 (0.14), residues: 1552 sheet: 0.32 (0.39), residues: 152 loop : -1.30 (0.18), residues: 1000 ********************** 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 332 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 328 time to evaluate : 2.833 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 329 average time/residue: 0.4101 time to fit residues: 197.1111 Evaluate side-chains 326 residues out of total 2368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 323 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2245 time to fit residues: 4.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 196 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN I 293 GLN M 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.133013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.098615 restraints weight = 25086.615| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.28 r_work: 0.2495 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2968 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= 0.154 Angle : 0.466 5.564 30460 Z= 0.245 Chirality : 0.040 0.120 3380 Planarity : 0.004 0.041 3844 Dihedral : 5.363 59.089 3084 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.37 % Rotamer Outliers : 0.13 % 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: 0.73 (0.17), residues: 2704 helix: 1.62 (0.14), residues: 1552 sheet: 0.17 (0.40), residues: 148 loop : -1.32 (0.18), residues: 1004 =============================================================================== Job complete usr+sys time: 4832.11 seconds wall clock time: 87 minutes 49.51 seconds (5269.51 seconds total)