Starting phenix.real_space_refine on Sat Aug 10 18:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8n_24319/08_2024/7r8n_24319.cif" } resolution = 3.55 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= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 18907 2.51 5 N 4913 2.21 5 O 5764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 702": "OE1" <-> "OE2" Residue "E GLU 773": "OE1" <-> "OE2" Residue "E TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 950": "OD1" <-> "OD2" Residue "E ASP 985": "OD1" <-> "OD2" Residue "E GLU 988": "OE1" <-> "OE2" Residue "E GLU 990": "OE1" <-> "OE2" Residue "E ASP 994": "OD1" <-> "OD2" Residue "E GLU 1017": "OE1" <-> "OE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "P TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29719 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "E" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7945 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 999 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 23.46, per 1000 atoms: 0.79 Number of scatterers: 29719 At special positions: 0 Unit cell: (150.337, 137.302, 175.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5764 8.00 N 4913 7.00 C 18907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 95 " 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 Atom "HETATM29493 O5 NAG B1303 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 801 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 717 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 282 " " NAG E1304 " - " ASN E 616 " " NAG E1305 " - " ASN E 657 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1098 " " NAG E1309 " - " ASN E1134 " " NAG E1310 " - " ASN E 61 " " NAG F 1 " - " ASN B 234 " " NAG G 1 " - " ASN B 717 " Time building additional restraints: 12.76 Conformation dependent library (CDL) restraints added in 5.9 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 69 sheets defined 20.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 removed outlier: 4.082A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.608A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.860A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.408A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.791A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.451A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 removed outlier: 4.234A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.630A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.604A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.512A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.817A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.513A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.634A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 620 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 removed outlier: 4.065A pdb=" N GLY E 891 " --> pdb=" O PHE E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.378A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.223A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.609A pdb=" N ASP M 89 " --> pdb=" O ARG M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 106 Processing helix chain 'N' and resid 82 through 86 removed outlier: 3.506A pdb=" N ASP N 85 " --> pdb=" O GLN N 82 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU N 86 " --> pdb=" O ALA N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 86' Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.596A pdb=" N ASP O 89 " --> pdb=" O ARG O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.931A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.740A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 587 " --> pdb=" O ASP E 574 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.531A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 229 removed outlier: 6.649A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.437A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 120 removed outlier: 4.101A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.988A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.922A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.748A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 376 through 378 removed outlier: 4.090A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.043A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.714A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 719 through 728 removed outlier: 3.518A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.110A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.795A pdb=" N LYS A 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.745A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.527A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.506A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.421A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.576A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.971A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.396A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.877A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.453A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.860A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.505A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.280A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.528A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.159A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 36 through 37 removed outlier: 8.006A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.505A pdb=" N PHE E 55 " --> pdb=" O GLN E 271 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 271 " --> pdb=" O PHE E 55 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.334A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE E 238 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 237 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE E 106 " --> pdb=" O ARG E 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN E 239 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TRP E 104 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU E 241 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 118 through 120 removed outlier: 4.297A pdb=" N VAL E 127 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR E 170 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU E 132 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N CYS E 166 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN E 134 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASN E 164 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 201 through 204 removed outlier: 3.763A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 313 through 319 removed outlier: 6.751A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 595 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 593 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 376 through 378 removed outlier: 4.081A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AF5, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.589A pdb=" N SER E 721 " --> pdb=" O THR E1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR E 723 " --> pdb=" O HIS E1064 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS E1064 " --> pdb=" O THR E 723 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E1062 " --> pdb=" O GLU E 725 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E 727 " --> pdb=" O VAL E1060 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL E1060 " --> pdb=" O LEU E 727 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR E 859 " --> pdb=" O SER E 735 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 1081 through 1082 removed outlier: 4.511A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 1093 through 1096 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.596A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS H 22 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.083A pdb=" N ILE H 12 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.083A pdb=" N ILE H 12 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N CYS H 95 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TRP H 121 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG H 97 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 11 through 13 Processing sheet with id=AG4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG5, first strand: chain 'L' and resid 48 through 52 removed outlier: 5.129A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.835A pdb=" N THR M 68 " --> pdb=" O GLN M 81 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 45 through 51 removed outlier: 5.042A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG9, first strand: chain 'N' and resid 48 through 52 removed outlier: 5.256A pdb=" N LEU N 49 " --> pdb=" O GLN N 40 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN N 40 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN N 41 " --> pdb=" O ASP N 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP N 88 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.511A pdb=" N MET O 82 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR O 68 " --> pdb=" O GLN O 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.486A pdb=" N TYR O 58 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 50 " --> pdb=" O TYR O 58 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N CYS O 95 " --> pdb=" O TRP O 121 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TRP O 121 " --> pdb=" O CYS O 95 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG O 97 " --> pdb=" O ASP O 119 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 58 through 59 removed outlier: 4.486A pdb=" N TYR O 58 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL O 50 " --> pdb=" O TYR O 58 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 11 through 13 Processing sheet with id=AH5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AH6, first strand: chain 'P' and resid 48 through 52 removed outlier: 6.570A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2742 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: 13.76 Time building geometry restraints manager: 13.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8617 1.34 - 1.47: 8566 1.47 - 1.60: 13039 1.60 - 1.73: 1 1.73 - 1.87: 171 Bond restraints: 30394 Sorted by residual: bond pdb=" N GLN N 6 " pdb=" CA GLN N 6 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.40e+01 bond pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.75e+01 bond pdb=" N PHE E 329 " pdb=" CA PHE E 329 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL L 11 " pdb=" CA VAL L 11 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL P 54 " pdb=" CA VAL P 54 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.16e+01 ... (remaining 30389 not shown) Histogram of bond angle deviations from ideal: 91.22 - 101.05: 40 101.05 - 110.87: 9795 110.87 - 120.69: 20015 120.69 - 130.52: 11452 130.52 - 140.34: 91 Bond angle restraints: 41393 Sorted by residual: angle pdb=" CA PRO A 272 " pdb=" N PRO A 272 " pdb=" CD PRO A 272 " ideal model delta sigma weight residual 112.00 98.56 13.44 1.40e+00 5.10e-01 9.21e+01 angle pdb=" N CYS E 525 " pdb=" CA CYS E 525 " pdb=" C CYS E 525 " ideal model delta sigma weight residual 107.73 118.60 -10.87 1.34e+00 5.57e-01 6.58e+01 angle pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" O GLY A 502 " ideal model delta sigma weight residual 122.22 117.15 5.07 6.50e-01 2.37e+00 6.09e+01 angle pdb=" CA GLN E 563 " pdb=" CB GLN E 563 " pdb=" CG GLN E 563 " ideal model delta sigma weight residual 114.10 128.70 -14.60 2.00e+00 2.50e-01 5.33e+01 angle pdb=" N ARG B1014 " pdb=" CA ARG B1014 " pdb=" C ARG B1014 " ideal model delta sigma weight residual 111.36 103.70 7.66 1.09e+00 8.42e-01 4.94e+01 ... (remaining 41388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16876 17.98 - 35.97: 1123 35.97 - 53.95: 303 53.95 - 71.94: 80 71.94 - 89.92: 44 Dihedral angle restraints: 18426 sinusoidal: 7398 harmonic: 11028 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -4.05 -81.95 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -10.03 -75.97 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 18423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 4556 0.177 - 0.354: 202 0.354 - 0.531: 14 0.531 - 0.708: 7 0.708 - 0.885: 1 Chirality restraints: 4780 Sorted by residual: chirality pdb=" CB ILE B 882 " pdb=" CA ILE B 882 " pdb=" CG1 ILE B 882 " pdb=" CG2 ILE B 882 " both_signs ideal model delta sigma weight residual False 2.64 1.76 0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CB ILE B 666 " pdb=" CA ILE B 666 " pdb=" CG1 ILE B 666 " pdb=" CG2 ILE B 666 " both_signs ideal model delta sigma weight residual False 2.64 1.99 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.67e+00 ... (remaining 4777 not shown) Planarity restraints: 5355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO A 272 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 14 " -0.093 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PRO P 15 " 0.243 5.00e-02 4.00e+02 pdb=" CA PRO P 15 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO P 15 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E1052 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO E1053 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO E1053 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO E1053 " -0.073 5.00e-02 4.00e+02 ... (remaining 5352 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1233 2.70 - 3.25: 28937 3.25 - 3.80: 47504 3.80 - 4.35: 59311 4.35 - 4.90: 98126 Nonbonded interactions: 235111 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.148 3.040 nonbonded pdb=" O GLU A 484 " pdb=" OH TYR H 58 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.188 3.040 nonbonded pdb=" O TYR E 38 " pdb=" OH TYR E 204 " model vdw 2.196 3.040 nonbonded pdb=" O GLU E 484 " pdb=" OH TYR M 58 " model vdw 2.216 3.040 ... (remaining 235106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 1140 or resid 1301 through 1308)) selection = (chain 'E' and (resid 15 through 1140 or resid 1301 through 1308)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.850 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 92.330 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.160 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 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 : 0.008 0.125 30394 Z= 0.520 Angle : 1.528 24.043 41393 Z= 0.852 Chirality : 0.089 0.885 4780 Planarity : 0.011 0.145 5324 Dihedral : 14.068 89.924 11229 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.48 % Allowed : 1.23 % Favored : 97.30 % Cbeta Deviations : 0.20 % 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: -1.20 (0.12), residues: 3753 helix: -0.05 (0.17), residues: 681 sheet: 0.18 (0.19), residues: 669 loop : -1.37 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP P 38 HIS 0.033 0.003 HIS E1048 PHE 0.074 0.005 PHE L 102 TYR 0.078 0.004 TYR A 904 ARG 0.017 0.002 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 618 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.5968 (m-30) cc_final: 0.5473 (m-30) REVERT: A 506 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6145 (mt0) REVERT: A 740 MET cc_start: 0.5664 (tpp) cc_final: 0.5277 (tpp) REVERT: A 814 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6746 (mmtt) REVERT: A 928 ASN cc_start: 0.7419 (m110) cc_final: 0.7108 (m-40) REVERT: A 977 LEU cc_start: 0.7538 (tp) cc_final: 0.7314 (tp) REVERT: B 349 SER cc_start: 0.7767 (t) cc_final: 0.7537 (p) REVERT: B 529 LYS cc_start: 0.8112 (mppt) cc_final: 0.7581 (tptp) REVERT: B 977 LEU cc_start: 0.7503 (tp) cc_final: 0.7134 (tp) REVERT: B 1048 HIS cc_start: 0.6745 (t70) cc_final: 0.6297 (t70) REVERT: E 118 LEU cc_start: 0.7069 (tp) cc_final: 0.6846 (tp) REVERT: E 759 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6240 (t80) REVERT: E 810 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7367 (p) REVERT: E 814 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7290 (mmtt) REVERT: L 94 PHE cc_start: 0.4021 (t80) cc_final: 0.3253 (t80) outliers start: 47 outliers final: 9 residues processed: 646 average time/residue: 0.3839 time to fit residues: 398.2764 Evaluate side-chains 422 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 408 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 738 CYS Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 810 SER Chi-restraints excluded: chain E residue 811 LYS Chi-restraints excluded: chain E residue 813 SER Chi-restraints excluded: chain E residue 814 LYS Chi-restraints excluded: chain L residue 41 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1011 GLN A1108 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 655 HIS B 901 GLN B1023 ASN B1101 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 31 ASN P 98 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30394 Z= 0.371 Angle : 0.851 13.558 41393 Z= 0.446 Chirality : 0.055 0.595 4780 Planarity : 0.007 0.075 5324 Dihedral : 8.474 71.772 4856 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.18 % Allowed : 12.04 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3753 helix: 0.04 (0.19), residues: 684 sheet: -0.22 (0.18), residues: 741 loop : -1.38 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 47 HIS 0.012 0.002 HIS A1064 PHE 0.038 0.003 PHE B 898 TYR 0.032 0.003 TYR E 37 ARG 0.007 0.001 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 492 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2051 (mmp) cc_final: 0.1803 (mmt) REVERT: A 506 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: A 651 ILE cc_start: 0.7971 (pt) cc_final: 0.7714 (pt) REVERT: A 740 MET cc_start: 0.5922 (tpp) cc_final: 0.5499 (tpt) REVERT: B 269 TYR cc_start: 0.3762 (OUTLIER) cc_final: 0.3125 (m-10) REVERT: B 529 LYS cc_start: 0.8192 (mppt) cc_final: 0.7406 (mmmt) REVERT: B 751 ASN cc_start: 0.8269 (m-40) cc_final: 0.7942 (m-40) REVERT: B 898 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5315 (t80) REVERT: B 1048 HIS cc_start: 0.6994 (t70) cc_final: 0.6278 (t70) REVERT: E 118 LEU cc_start: 0.7279 (tp) cc_final: 0.7073 (tp) REVERT: E 269 TYR cc_start: 0.3522 (OUTLIER) cc_final: 0.3125 (m-10) REVERT: H 89 ASP cc_start: 0.4779 (m-30) cc_final: 0.4515 (m-30) REVERT: L 41 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6870 (pt0) REVERT: L 94 PHE cc_start: 0.4313 (t80) cc_final: 0.3445 (t80) REVERT: M 19 ARG cc_start: 0.6476 (tpt170) cc_final: 0.6274 (tpp80) REVERT: M 89 ASP cc_start: 0.5068 (m-30) cc_final: 0.4719 (m-30) REVERT: N 17 GLN cc_start: 0.7978 (pp30) cc_final: 0.7563 (pp30) REVERT: P 90 TYR cc_start: 0.6886 (m-80) cc_final: 0.6485 (m-80) outliers start: 101 outliers final: 70 residues processed: 547 average time/residue: 0.3903 time to fit residues: 352.6246 Evaluate side-chains 466 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 391 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 269 TYR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 313 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 9.9990 chunk 368 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 338 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 422 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1023 ASN B 271 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN B1058 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 99 ASN E 493 GLN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 655 HIS E 675 GLN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN E 901 GLN E 955 ASN E1010 GLN ** E1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN N 6 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 ASN ** P 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 30394 Z= 0.396 Angle : 0.820 15.551 41393 Z= 0.429 Chirality : 0.054 0.540 4780 Planarity : 0.006 0.067 5324 Dihedral : 7.748 67.880 4837 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.49 % Rotamer: Outliers : 5.57 % Allowed : 14.81 % Favored : 79.62 % 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: -1.43 (0.13), residues: 3753 helix: -0.07 (0.19), residues: 678 sheet: -0.15 (0.19), residues: 657 loop : -1.51 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP O 47 HIS 0.009 0.002 HIS E 655 PHE 0.030 0.003 PHE B 898 TYR 0.026 0.003 TYR A 380 ARG 0.020 0.001 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 454 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2831 (mmp) cc_final: 0.2256 (mmt) REVERT: A 376 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7701 (p) REVERT: A 506 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6736 (mt0) REVERT: A 858 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8465 (pp) REVERT: A 900 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6035 (mtp) REVERT: B 118 LEU cc_start: 0.7672 (mp) cc_final: 0.6965 (tp) REVERT: B 214 ARG cc_start: 0.2346 (mmm160) cc_final: 0.1359 (mmm160) REVERT: B 529 LYS cc_start: 0.8224 (mppt) cc_final: 0.7408 (mmmt) REVERT: B 870 ILE cc_start: 0.8074 (mm) cc_final: 0.7814 (mt) REVERT: B 898 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5317 (t80) REVERT: B 1089 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: E 118 LEU cc_start: 0.7574 (tp) cc_final: 0.7347 (tp) REVERT: E 203 ILE cc_start: 0.8555 (mt) cc_final: 0.8044 (tp) REVERT: E 237 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6755 (mmm160) REVERT: E 298 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6159 (mm-30) REVERT: E 376 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7768 (p) REVERT: E 428 ASP cc_start: 0.7848 (p0) cc_final: 0.7536 (p0) REVERT: E 759 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6941 (t80) REVERT: E 967 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7596 (t) REVERT: H 51 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6572 (mp) REVERT: H 123 GLN cc_start: 0.5872 (mp10) cc_final: 0.5368 (tm-30) REVERT: L 41 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6769 (pt0) REVERT: L 81 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5558 (tt) REVERT: L 94 PHE cc_start: 0.4129 (t80) cc_final: 0.2669 (t80) REVERT: M 19 ARG cc_start: 0.6652 (tpt170) cc_final: 0.6431 (tpp80) REVERT: M 89 ASP cc_start: 0.5271 (m-30) cc_final: 0.4915 (m-30) REVERT: N 17 GLN cc_start: 0.8076 (pp30) cc_final: 0.7744 (pp30) REVERT: N 94 PHE cc_start: 0.5208 (t80) cc_final: 0.5002 (t80) REVERT: P 90 TYR cc_start: 0.7215 (m-80) cc_final: 0.6944 (m-80) REVERT: P 102 PHE cc_start: 0.5695 (m-80) cc_final: 0.5365 (m-10) outliers start: 177 outliers final: 107 residues processed: 571 average time/residue: 0.3832 time to fit residues: 361.8298 Evaluate side-chains 500 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 380 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 655 HIS Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 29 ASP Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 32 ASN Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 63 ASP Chi-restraints excluded: chain P residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 762 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 30394 Z= 0.437 Angle : 0.808 13.404 41393 Z= 0.423 Chirality : 0.054 0.519 4780 Planarity : 0.006 0.065 5324 Dihedral : 7.608 64.191 4834 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.89 % Favored : 92.09 % Rotamer: Outliers : 5.82 % Allowed : 17.67 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3753 helix: -0.26 (0.19), residues: 678 sheet: -0.26 (0.20), residues: 666 loop : -1.69 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 121 HIS 0.025 0.002 HIS E 655 PHE 0.025 0.002 PHE E 168 TYR 0.024 0.003 TYR E 37 ARG 0.007 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 416 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6759 (mt0) REVERT: A 763 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 858 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8526 (pp) REVERT: A 900 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.5888 (mtp) REVERT: B 214 ARG cc_start: 0.2601 (mmm160) cc_final: 0.1690 (mmm160) REVERT: B 529 LYS cc_start: 0.8338 (mppt) cc_final: 0.7484 (mmmt) REVERT: B 729 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (t) REVERT: B 898 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5150 (t80) REVERT: B 1089 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: E 118 LEU cc_start: 0.7700 (tp) cc_final: 0.7101 (pp) REVERT: E 189 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5077 (mp) REVERT: E 203 ILE cc_start: 0.8569 (mt) cc_final: 0.8048 (tp) REVERT: E 298 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6147 (mm-30) REVERT: E 428 ASP cc_start: 0.7944 (p0) cc_final: 0.7595 (p0) REVERT: E 434 ILE cc_start: 0.9137 (mp) cc_final: 0.8933 (mt) REVERT: E 1055 SER cc_start: 0.8280 (t) cc_final: 0.7946 (p) REVERT: H 51 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6694 (mp) REVERT: H 123 GLN cc_start: 0.6212 (mp10) cc_final: 0.5497 (tm-30) REVERT: L 41 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6709 (pt0) REVERT: L 81 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5717 (tt) REVERT: L 90 TYR cc_start: 0.7635 (m-80) cc_final: 0.6910 (m-80) REVERT: L 94 PHE cc_start: 0.4934 (t80) cc_final: 0.3253 (t80) REVERT: M 89 ASP cc_start: 0.5197 (m-30) cc_final: 0.4970 (m-30) REVERT: N 17 GLN cc_start: 0.8220 (pp30) cc_final: 0.7940 (pp30) REVERT: N 41 GLN cc_start: 0.6695 (pp30) cc_final: 0.6418 (pp30) REVERT: N 102 PHE cc_start: 0.6812 (m-80) cc_final: 0.6594 (m-80) REVERT: P 100 ARG cc_start: 0.6687 (ptp-170) cc_final: 0.5955 (mtt180) outliers start: 185 outliers final: 117 residues processed: 550 average time/residue: 0.3729 time to fit residues: 339.7990 Evaluate side-chains 494 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 365 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 534 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 592 PHE Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 734 THR Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1130 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 0.6980 chunk 325 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 928 ASN A 949 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 409 GLN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 32 ASN O 73 ASN P 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30394 Z= 0.222 Angle : 0.708 14.737 41393 Z= 0.363 Chirality : 0.050 0.515 4780 Planarity : 0.005 0.065 5324 Dihedral : 7.138 59.588 4834 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.77 % Favored : 93.21 % Rotamer: Outliers : 4.87 % Allowed : 19.81 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 3753 helix: -0.05 (0.20), residues: 687 sheet: -0.34 (0.19), residues: 696 loop : -1.52 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 47 HIS 0.008 0.001 HIS B1048 PHE 0.020 0.002 PHE E1095 TYR 0.021 0.002 TYR E1067 ARG 0.007 0.001 ARG N 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 446 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.6967 (m) cc_final: 0.6712 (m) REVERT: A 376 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 900 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5772 (mtp) REVERT: B 214 ARG cc_start: 0.2515 (mmm160) cc_final: 0.1511 (mmm160) REVERT: B 529 LYS cc_start: 0.8283 (mppt) cc_final: 0.7471 (mmmt) REVERT: B 697 MET cc_start: 0.5025 (ptm) cc_final: 0.4772 (ptm) REVERT: B 751 ASN cc_start: 0.8340 (m-40) cc_final: 0.8113 (m-40) REVERT: B 759 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7216 (t80) REVERT: B 870 ILE cc_start: 0.8237 (mm) cc_final: 0.7990 (mt) REVERT: B 900 MET cc_start: 0.5779 (mpp) cc_final: 0.5427 (mpp) REVERT: E 118 LEU cc_start: 0.7625 (tp) cc_final: 0.7372 (tp) REVERT: E 189 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5286 (mp) REVERT: E 203 ILE cc_start: 0.8425 (mt) cc_final: 0.7913 (tp) REVERT: E 376 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7870 (p) REVERT: E 428 ASP cc_start: 0.7843 (p0) cc_final: 0.7484 (p0) REVERT: E 511 VAL cc_start: 0.8470 (t) cc_final: 0.8215 (t) REVERT: E 759 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7008 (t80) REVERT: H 3 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7056 (mp10) REVERT: H 45 LEU cc_start: 0.7934 (mp) cc_final: 0.7597 (mt) REVERT: H 51 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6503 (mp) REVERT: L 41 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6464 (pt0) REVERT: L 81 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5521 (tt) REVERT: L 90 TYR cc_start: 0.7548 (m-80) cc_final: 0.6736 (m-80) REVERT: L 94 PHE cc_start: 0.4520 (t80) cc_final: 0.3002 (t80) REVERT: M 19 ARG cc_start: 0.6630 (tpt170) cc_final: 0.6201 (tpp80) REVERT: M 89 ASP cc_start: 0.4880 (m-30) cc_final: 0.4599 (m-30) REVERT: N 17 GLN cc_start: 0.8078 (pp30) cc_final: 0.7830 (pp30) REVERT: O 29 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7442 (t) REVERT: P 41 GLN cc_start: 0.7359 (pm20) cc_final: 0.7059 (pm20) REVERT: P 90 TYR cc_start: 0.7156 (m-80) cc_final: 0.6374 (m-80) REVERT: P 94 PHE cc_start: 0.4652 (t80) cc_final: 0.3349 (t80) outliers start: 155 outliers final: 96 residues processed: 551 average time/residue: 0.3945 time to fit residues: 356.3734 Evaluate side-chains 485 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 379 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 898 PHE Chi-restraints excluded: chain B residue 928 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 595 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 SER Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 860 VAL Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1051 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 ASP Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 32 ASN Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 105 SER Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 63 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7044 > 50: distance: 99 - 104: 10.383 distance: 104 - 105: 4.804 distance: 104 - 110: 19.966 distance: 105 - 106: 7.966 distance: 105 - 108: 10.773 distance: 106 - 107: 37.299 distance: 106 - 111: 5.271 distance: 108 - 109: 33.236 distance: 109 - 110: 26.401 distance: 112 - 113: 19.161 distance: 112 - 115: 40.150 distance: 113 - 114: 40.273 distance: 113 - 116: 8.513 distance: 116 - 117: 9.226 distance: 117 - 118: 7.571 distance: 118 - 119: 22.999 distance: 118 - 120: 45.735 distance: 120 - 121: 7.586 distance: 121 - 122: 19.017 distance: 121 - 124: 9.321 distance: 122 - 123: 25.743 distance: 122 - 131: 13.302 distance: 124 - 125: 26.340 distance: 125 - 126: 20.830 distance: 125 - 127: 9.033 distance: 126 - 128: 25.795 distance: 127 - 129: 5.235 distance: 128 - 130: 18.273 distance: 129 - 130: 13.882 distance: 131 - 132: 33.459 distance: 132 - 133: 25.481 distance: 133 - 134: 19.433 distance: 133 - 137: 18.224 distance: 137 - 138: 17.627 distance: 138 - 139: 21.449 distance: 138 - 141: 3.394 distance: 139 - 142: 10.753 distance: 142 - 143: 8.439 distance: 143 - 144: 13.781 distance: 143 - 146: 13.630 distance: 144 - 145: 9.015 distance: 144 - 150: 9.643 distance: 146 - 147: 10.353 distance: 147 - 148: 4.053 distance: 147 - 149: 18.916 distance: 150 - 151: 7.614 distance: 151 - 152: 8.964 distance: 151 - 154: 21.895 distance: 152 - 159: 9.851 distance: 154 - 155: 17.656 distance: 155 - 156: 6.586 distance: 156 - 157: 14.551 distance: 156 - 158: 13.957 distance: 159 - 160: 11.424 distance: 159 - 165: 22.599 distance: 160 - 161: 12.773 distance: 160 - 163: 13.459 distance: 161 - 162: 18.439 distance: 161 - 166: 36.222 distance: 163 - 164: 10.895 distance: 164 - 165: 3.662 distance: 166 - 167: 15.585 distance: 167 - 168: 11.873 distance: 167 - 170: 17.277 distance: 168 - 169: 11.234 distance: 168 - 174: 19.818 distance: 170 - 171: 16.383 distance: 171 - 172: 6.310 distance: 171 - 173: 10.356