Starting phenix.real_space_refine on Thu Mar 21 23:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5d_26348/03_2024/7u5d_26348.pdb" } resolution = 3.52 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= 0.002 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: 5 Type Number sf(0) Gaussians P 140 5.49 5 S 130 5.16 5 C 19529 2.51 5 N 5570 2.21 5 O 6146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 46": "OD1" <-> "OD2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 286": "OD1" <-> "OD2" Residue "J PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31515 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1285 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 23, 'rna3p_pyr': 11} Link IDs: {'rna2p': 26, 'rna3p': 33} Chain: "2" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1127 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan2': 1, ' DA:plan2': 1, ' DC:plan': 1, ' DA:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "3" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4970 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 35, 'TRANS': 594} Chain breaks: 3 Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "E" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "F" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2711 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 17, 'TRANS': 324} Chain: "G" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2390 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 15, 'TRANS': 284} Chain breaks: 3 Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1631 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3084 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 1 Chain: "J" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2980 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 16.58, per 1000 atoms: 0.53 Number of scatterers: 31515 At special positions: 0 Unit cell: (147.537, 196.425, 174.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 140 15.00 O 6146 8.00 N 5570 7.00 C 19529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 133 O4' A 1 7 .*. O " rejected from bonding due to valence issues. Atom "ATOM 85 O5' G 1 5 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.55 Conformation dependent library (CDL) restraints added in 5.3 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 39.7% alpha, 14.3% beta 31 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 9.50 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 removed outlier: 4.225A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 Processing helix chain 'A' and resid 51 through 52 No H-bonds generated for 'chain 'A' and resid 51 through 52' Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.627A pdb=" N VAL A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.604A pdb=" N SER A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.852A pdb=" N THR A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.976A pdb=" N GLY A 119 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.704A pdb=" N THR A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 173 through 187 removed outlier: 4.005A pdb=" N GLN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.780A pdb=" N ASN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.765A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 380 through 394 Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.897A pdb=" N LEU A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 removed outlier: 3.732A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 668 through 676 removed outlier: 3.775A pdb=" N MET A 672 " --> pdb=" O ASN A 668 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.858A pdb=" N LEU B 64 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.790A pdb=" N VAL B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 removed outlier: 3.530A pdb=" N LEU B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.502A pdb=" N TRP B 142 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 143 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 145 " --> pdb=" O TRP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 4.385A pdb=" N ARG B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.529A pdb=" N GLU B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.761A pdb=" N ALA B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 4.140A pdb=" N ASN B 270 " --> pdb=" O TRP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'C' and resid 60 through 65 removed outlier: 3.952A pdb=" N LEU C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 120 removed outlier: 3.796A pdb=" N VAL C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.710A pdb=" N ASN C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 removed outlier: 3.510A pdb=" N TRP C 142 " --> pdb=" O ILE C 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 180 through 195 removed outlier: 3.510A pdb=" N GLU C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.834A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.839A pdb=" N THR C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.835A pdb=" N LEU D 64 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.812A pdb=" N VAL D 110 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.592A pdb=" N ASN D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY D 138 " --> pdb=" O ASN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.591A pdb=" N TRP D 142 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG D 143 " --> pdb=" O TRP D 140 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 145 " --> pdb=" O TRP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.543A pdb=" N GLU D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.838A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.744A pdb=" N THR D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 325 through 337 Processing helix chain 'E' and resid 60 through 65 removed outlier: 3.846A pdb=" N LEU E 64 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.770A pdb=" N VAL E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 removed outlier: 3.504A pdb=" N ASN E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.512A pdb=" N TRP E 142 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG E 143 " --> pdb=" O TRP E 140 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 145 " --> pdb=" O TRP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 195 Processing helix chain 'E' and resid 253 through 262 removed outlier: 3.764A pdb=" N ALA E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 299 through 305 removed outlier: 3.538A pdb=" N LEU E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR E 305 " --> pdb=" O TYR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 104 through 120 Processing helix chain 'F' and resid 123 through 138 removed outlier: 3.797A pdb=" N GLY F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.521A pdb=" N TRP F 142 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG F 143 " --> pdb=" O TRP F 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN F 145 " --> pdb=" O TRP F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.718A pdb=" N ALA F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 297 Processing helix chain 'F' and resid 299 through 305 removed outlier: 3.528A pdb=" N LEU F 303 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 305 " --> pdb=" O TYR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.542A pdb=" N ASN G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 removed outlier: 6.504A pdb=" N ARG G 143 " --> pdb=" O TRP G 140 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN G 145 " --> pdb=" O TRP G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 4.202A pdb=" N ARG G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU G 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 166 through 170' Processing helix chain 'G' and resid 180 through 195 Processing helix chain 'G' and resid 253 through 262 removed outlier: 3.754A pdb=" N ALA G 260 " --> pdb=" O LYS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 299 through 305 removed outlier: 3.527A pdb=" N LEU G 303 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR G 305 " --> pdb=" O TYR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.912A pdb=" N GLY H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 74 through 83 removed outlier: 3.528A pdb=" N GLN H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.774A pdb=" N LEU H 109 " --> pdb=" O ASN H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 132 removed outlier: 3.558A pdb=" N ARG H 117 " --> pdb=" O PHE H 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS H 129 " --> pdb=" O LYS H 125 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 30 through 46 removed outlier: 3.537A pdb=" N VAL I 38 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP I 41 " --> pdb=" O SER I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 52 removed outlier: 4.138A pdb=" N ALA I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 removed outlier: 3.918A pdb=" N ASN I 61 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE I 62 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE I 63 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 83 removed outlier: 3.561A pdb=" N ARG I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 129 through 134 Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.834A pdb=" N LEU I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 251 removed outlier: 4.039A pdb=" N LYS I 251 " --> pdb=" O ARG I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 257 through 261 Proline residue: I 260 - end of helix No H-bonds generated for 'chain 'I' and resid 257 through 261' Processing helix chain 'I' and resid 262 through 276 removed outlier: 3.770A pdb=" N MET I 270 " --> pdb=" O GLU I 266 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL I 271 " --> pdb=" O LEU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 286 through 292 removed outlier: 4.099A pdb=" N VAL I 290 " --> pdb=" O ASP I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 300 Processing helix chain 'I' and resid 309 through 325 Processing helix chain 'I' and resid 341 through 348 Processing helix chain 'I' and resid 351 through 361 removed outlier: 3.710A pdb=" N VAL I 355 " --> pdb=" O SER I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 396 Processing helix chain 'J' and resid 14 through 25 Processing helix chain 'J' and resid 30 through 43 removed outlier: 3.728A pdb=" N HIS J 43 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'J' and resid 61 through 65 Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 89 through 94 removed outlier: 3.831A pdb=" N GLN J 92 " --> pdb=" O ARG J 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA J 94 " --> pdb=" O LEU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 102 Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 199 through 204 Processing helix chain 'J' and resid 205 through 207 No H-bonds generated for 'chain 'J' and resid 205 through 207' Processing helix chain 'J' and resid 221 through 236 Processing helix chain 'J' and resid 247 through 256 removed outlier: 4.686A pdb=" N ILE J 253 " --> pdb=" O LEU J 249 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY J 254 " --> pdb=" O THR J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 277 removed outlier: 4.440A pdb=" N TRP J 264 " --> pdb=" O PRO J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 285 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.585A pdb=" N VAL J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 300 Processing helix chain 'J' and resid 309 through 325 Processing helix chain 'J' and resid 340 through 348 Processing helix chain 'J' and resid 351 through 361 Processing helix chain 'J' and resid 385 through 396 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 removed outlier: 4.391A pdb=" N VAL A 219 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.517A pdb=" N ILE A 607 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP A 493 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 13.492A pdb=" N LEU A 491 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG A 489 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N HIS A 543 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 491 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU A 541 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP A 493 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE A 539 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU A 495 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 537 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 531 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS A 532 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR A 448 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 534 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A 446 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET A 536 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 444 " --> pdb=" O MET A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 208 removed outlier: 4.021A pdb=" N GLY A 636 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 662 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA A 634 " --> pdb=" O GLY A 662 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA A 664 " --> pdb=" O PRO A 632 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS A 666 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU A 630 " --> pdb=" O CYS A 666 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 8.681A pdb=" N CYS A 459 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 263 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 455 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512 removed outlier: 3.869A pdb=" N LYS A 511 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 22 current: chain 'B' and resid 150 through 156 Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 92 current: chain 'B' and resid 240 through 242 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB6, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'C' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 22 current: chain 'C' and resid 150 through 156 Processing sheet with id=AB8, first strand: chain 'C' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 92 current: chain 'C' and resid 240 through 242 Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AC1, first strand: chain 'C' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'D' and resid 7 through 8 Processing sheet with id=AC3, first strand: chain 'D' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 150 through 156 Processing sheet with id=AC4, first strand: chain 'D' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 92 current: chain 'D' and resid 240 through 242 Processing sheet with id=AC5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AC6, first strand: chain 'D' and resid 283 through 284 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 150 through 155 Processing sheet with id=AC9, first strand: chain 'E' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 83 through 92 current: chain 'E' and resid 240 through 242 Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AD2, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 150 through 156 Processing sheet with id=AD5, first strand: chain 'F' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 240 through 242 Processing sheet with id=AD6, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AD7, first strand: chain 'F' and resid 283 through 284 Processing sheet with id=AD8, first strand: chain 'G' and resid 7 through 8 Processing sheet with id=AD9, first strand: chain 'G' and resid 13 through 15 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 22 current: chain 'G' and resid 150 through 156 Processing sheet with id=AE1, first strand: chain 'G' and resid 30 through 31 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 83 through 92 current: chain 'G' and resid 240 through 242 Processing sheet with id=AE2, first strand: chain 'G' and resid 72 through 74 removed outlier: 7.400A pdb=" N VAL G 36 " --> pdb=" O LYS H 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 283 through 284 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 Processing sheet with id=AE6, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AE7, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE8, first strand: chain 'I' and resid 96 through 97 Processing sheet with id=AE9, first strand: chain 'I' and resid 338 through 340 Processing sheet with id=AF1, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AF2, first strand: chain 'J' and resid 338 through 339 1077 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 11.77 Time building geometry restraints manager: 13.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4888 1.30 - 1.43: 9637 1.43 - 1.56: 17577 1.56 - 1.68: 287 1.68 - 1.81: 172 Bond restraints: 32561 Sorted by residual: bond pdb=" O3' A 1 4 " pdb=" P G 1 5 " ideal model delta sigma weight residual 1.607 1.718 -0.111 1.50e-02 4.44e+03 5.49e+01 bond pdb=" CA ILE J 316 " pdb=" C ILE J 316 " ideal model delta sigma weight residual 1.523 1.446 0.078 1.27e-02 6.20e+03 3.74e+01 bond pdb=" CA ILE I 316 " pdb=" C ILE I 316 " ideal model delta sigma weight residual 1.524 1.445 0.078 1.30e-02 5.92e+03 3.62e+01 bond pdb=" CA LEU J 315 " pdb=" C LEU J 315 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.53e+01 bond pdb=" CA LEU I 315 " pdb=" C LEU I 315 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 ... (remaining 32556 not shown) Histogram of bond angle deviations from ideal: 95.91 - 104.07: 859 104.07 - 112.22: 15545 112.22 - 120.37: 16308 120.37 - 128.53: 11648 128.53 - 136.68: 429 Bond angle restraints: 44789 Sorted by residual: angle pdb=" C ARG J 6 " pdb=" N PRO J 7 " pdb=" CA PRO J 7 " ideal model delta sigma weight residual 120.52 133.51 -12.99 9.90e-01 1.02e+00 1.72e+02 angle pdb=" C CYS J 129 " pdb=" N PRO J 130 " pdb=" CA PRO J 130 " ideal model delta sigma weight residual 119.47 133.51 -14.04 1.16e+00 7.43e-01 1.46e+02 angle pdb=" C TRP B 176 " pdb=" N PRO B 177 " pdb=" CA PRO B 177 " ideal model delta sigma weight residual 119.89 131.22 -11.33 1.02e+00 9.61e-01 1.23e+02 angle pdb=" C TRP F 176 " pdb=" N PRO F 177 " pdb=" CA PRO F 177 " ideal model delta sigma weight residual 119.90 131.16 -11.26 1.02e+00 9.61e-01 1.22e+02 angle pdb=" C MET H 139 " pdb=" N PRO H 140 " pdb=" CA PRO H 140 " ideal model delta sigma weight residual 120.98 132.58 -11.60 1.07e+00 8.73e-01 1.18e+02 ... (remaining 44784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.51: 18425 31.51 - 63.02: 682 63.02 - 94.53: 103 94.53 - 126.04: 3 126.04 - 157.54: 7 Dihedral angle restraints: 19220 sinusoidal: 8751 harmonic: 10469 Sorted by residual: dihedral pdb=" O4' U 1 43 " pdb=" C1' U 1 43 " pdb=" N1 U 1 43 " pdb=" C2 U 1 43 " ideal model delta sinusoidal sigma weight residual 232.00 81.57 150.43 1 1.70e+01 3.46e-03 6.21e+01 dihedral pdb=" O4' U 1 45 " pdb=" C1' U 1 45 " pdb=" N1 U 1 45 " pdb=" C2 U 1 45 " ideal model delta sinusoidal sigma weight residual 200.00 88.59 111.41 1 1.50e+01 4.44e-03 5.82e+01 dihedral pdb=" N CYS I 142 " pdb=" C CYS I 142 " pdb=" CA CYS I 142 " pdb=" CB CYS I 142 " ideal model delta harmonic sigma weight residual 122.80 136.32 -13.52 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 19217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3537 0.088 - 0.175: 1166 0.175 - 0.263: 167 0.263 - 0.351: 49 0.351 - 0.438: 11 Chirality restraints: 4930 Sorted by residual: chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA TYR A 93 " pdb=" N TYR A 93 " pdb=" C TYR A 93 " pdb=" CB TYR A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA CYS I 142 " pdb=" N CYS I 142 " pdb=" C CYS I 142 " pdb=" CB CYS I 142 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 4927 not shown) Planarity restraints: 5303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 93 " -0.137 2.00e-02 2.50e+03 7.18e-02 1.03e+02 pdb=" CG TYR A 93 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 93 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 93 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 93 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 93 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR A 93 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 93 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 205 " 0.031 2.00e-02 2.50e+03 6.20e-02 3.85e+01 pdb=" C ASP F 205 " -0.107 2.00e-02 2.50e+03 pdb=" O ASP F 205 " 0.041 2.00e-02 2.50e+03 pdb=" N VAL F 206 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 205 " 0.031 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C ASP G 205 " -0.107 2.00e-02 2.50e+03 pdb=" O ASP G 205 " 0.041 2.00e-02 2.50e+03 pdb=" N VAL G 206 " 0.036 2.00e-02 2.50e+03 ... (remaining 5300 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.37: 15 1.37 - 2.25: 85 2.25 - 3.13: 24361 3.13 - 4.02: 74955 4.02 - 4.90: 138625 Warning: very small nonbonded interaction distances. Nonbonded interactions: 238041 Sorted by model distance: nonbonded pdb=" C1' A 1 7 " pdb=" OE2 GLU A 508 " model vdw 0.483 3.470 nonbonded pdb=" P G 1 5 " pdb=" NH2 ARG A 566 " model vdw 0.704 3.480 nonbonded pdb=" CE2 PHE I 88 " pdb=" CD ARG J 395 " model vdw 0.779 3.740 nonbonded pdb=" CE1 PHE A 403 " pdb=" NH2 ARG I 373 " model vdw 0.799 3.420 nonbonded pdb=" O4' A 1 7 " pdb=" OE2 GLU A 508 " model vdw 0.947 3.040 ... (remaining 238036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'C' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'D' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'E' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = (chain 'F' and (resid 3 through 39 or resid 69 through 226 or resid 235 through \ 318 or resid 324 through 344)) selection = chain 'G' } ncs_group { reference = (chain 'I' and (resid 7 through 368 or resid 382 through 397)) selection = (chain 'J' and (resid 7 through 188 or resid 196 through 397)) } 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: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.510 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 86.470 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.150 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:2.810 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.013 0.111 32561 Z= 0.864 Angle : 1.650 17.579 44789 Z= 1.172 Chirality : 0.085 0.438 4930 Planarity : 0.009 0.093 5303 Dihedral : 15.664 157.545 12482 Min Nonbonded Distance : 0.483 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 0.20 % Allowed : 0.59 % Favored : 99.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 3565 helix: -0.54 (0.13), residues: 1187 sheet: 0.37 (0.21), residues: 505 loop : -0.15 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 180 HIS 0.008 0.000 HIS A 472 PHE 0.049 0.002 PHE A 206 TYR 0.137 0.002 TYR A 93 ARG 0.004 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 475 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: B 197 GLN cc_start: 0.8310 (tt0) cc_final: 0.8100 (tt0) REVERT: C 153 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7099 (mt-10) REVERT: D 111 MET cc_start: 0.8758 (mmm) cc_final: 0.8556 (mmp) REVERT: I 273 ASP cc_start: 0.7642 (m-30) cc_final: 0.7436 (m-30) REVERT: J 267 LEU cc_start: 0.7592 (mt) cc_final: 0.6782 (mt) outliers start: 6 outliers final: 3 residues processed: 480 average time/residue: 0.5116 time to fit residues: 367.4665 Evaluate side-chains 259 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 336 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS C 186 GLN D 285 HIS E 216 GLN E 231 HIS F 58 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS F 342 GLN G 70 GLN G 163 HIS I 141 GLN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32561 Z= 0.215 Angle : 0.660 14.889 44789 Z= 0.352 Chirality : 0.042 0.260 4930 Planarity : 0.005 0.067 5303 Dihedral : 17.276 166.970 5747 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.01 % Allowed : 5.85 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 3565 helix: 0.76 (0.14), residues: 1244 sheet: 0.34 (0.22), residues: 498 loop : -0.31 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 259 HIS 0.008 0.001 HIS B 293 PHE 0.017 0.002 PHE I 210 TYR 0.034 0.002 TYR J 232 ARG 0.023 0.001 ARG J 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 3.454 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: F 132 SER cc_start: 0.9132 (m) cc_final: 0.8750 (t) REVERT: J 315 LEU cc_start: 0.8452 (tt) cc_final: 0.8215 (tt) REVERT: J 384 HIS cc_start: 0.4294 (m-70) cc_final: 0.4047 (m-70) outliers start: 31 outliers final: 19 residues processed: 298 average time/residue: 0.4556 time to fit residues: 212.1638 Evaluate side-chains 237 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 163 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain J residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 337 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 300 optimal weight: 0.1980 chunk 334 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 270 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS F 95 ASN F 181 GLN I 154 HIS I 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32561 Z= 0.233 Angle : 0.603 9.728 44789 Z= 0.320 Chirality : 0.041 0.247 4930 Planarity : 0.005 0.052 5303 Dihedral : 17.028 175.490 5737 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.24 % Allowed : 6.64 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3565 helix: 1.06 (0.15), residues: 1255 sheet: 0.58 (0.24), residues: 453 loop : -0.64 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 259 HIS 0.033 0.001 HIS G 163 PHE 0.019 0.002 PHE I 88 TYR 0.021 0.001 TYR J 232 ARG 0.015 0.001 ARG J 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 3.352 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: C 301 TYR cc_start: 0.8915 (m-80) cc_final: 0.8683 (m-80) REVERT: C 309 GLN cc_start: 0.7389 (mm110) cc_final: 0.7137 (mm-40) REVERT: F 95 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (t0) REVERT: J 315 LEU cc_start: 0.8446 (tt) cc_final: 0.8195 (tt) REVERT: J 384 HIS cc_start: 0.4408 (m-70) cc_final: 0.4162 (m-70) outliers start: 38 outliers final: 23 residues processed: 262 average time/residue: 0.4647 time to fit residues: 190.7638 Evaluate side-chains 233 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 379 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 175 optimal weight: 0.0770 chunk 37 optimal weight: 0.0040 chunk 161 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 338 optimal weight: 6.9990 chunk 358 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN E 231 HIS F 58 ASN G 163 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32561 Z= 0.141 Angle : 0.539 10.242 44789 Z= 0.285 Chirality : 0.039 0.238 4930 Planarity : 0.004 0.049 5303 Dihedral : 16.902 179.750 5737 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.24 % Allowed : 7.16 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3565 helix: 1.23 (0.15), residues: 1259 sheet: 0.66 (0.24), residues: 458 loop : -0.66 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 259 HIS 0.013 0.001 HIS I 379 PHE 0.019 0.001 PHE I 63 TYR 0.027 0.001 TYR H 172 ARG 0.007 0.000 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 3.470 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: C 301 TYR cc_start: 0.8896 (m-80) cc_final: 0.8682 (m-80) REVERT: C 309 GLN cc_start: 0.7323 (mm110) cc_final: 0.7121 (mm-40) REVERT: F 132 SER cc_start: 0.9136 (m) cc_final: 0.8663 (t) REVERT: H 65 LYS cc_start: 0.7318 (ttmt) cc_final: 0.6341 (ttmt) REVERT: J 267 LEU cc_start: 0.7501 (mt) cc_final: 0.7172 (mt) REVERT: J 315 LEU cc_start: 0.8518 (tt) cc_final: 0.8236 (tt) REVERT: J 384 HIS cc_start: 0.4439 (m-70) cc_final: 0.4100 (m-70) outliers start: 38 outliers final: 23 residues processed: 257 average time/residue: 0.4681 time to fit residues: 189.4967 Evaluate side-chains 223 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 321 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN H 81 GLN I 400 HIS ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32561 Z= 0.265 Angle : 0.591 10.551 44789 Z= 0.311 Chirality : 0.041 0.243 4930 Planarity : 0.005 0.066 5303 Dihedral : 16.895 178.808 5737 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.37 % Allowed : 7.85 % Favored : 90.78 % 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: 0.06 (0.14), residues: 3565 helix: 1.15 (0.15), residues: 1255 sheet: 0.50 (0.24), residues: 465 loop : -0.86 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 259 HIS 0.024 0.001 HIS E 231 PHE 0.019 0.002 PHE B 20 TYR 0.018 0.001 TYR H 172 ARG 0.012 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 3.335 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: A 381 MET cc_start: 0.6924 (pmm) cc_final: 0.6572 (pmm) REVERT: A 399 ARG cc_start: 0.6825 (mmt180) cc_final: 0.6368 (mpt180) REVERT: B 199 ASP cc_start: 0.6897 (t0) cc_final: 0.6684 (t0) REVERT: G 70 GLN cc_start: 0.5084 (pp30) cc_final: 0.4738 (pp30) REVERT: J 315 LEU cc_start: 0.8424 (tt) cc_final: 0.8164 (tt) outliers start: 42 outliers final: 30 residues processed: 248 average time/residue: 0.4666 time to fit residues: 183.1766 Evaluate side-chains 230 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 347 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 358 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 166 optimal weight: 0.0010 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS H 81 GLN ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32561 Z= 0.220 Angle : 0.559 11.908 44789 Z= 0.295 Chirality : 0.040 0.240 4930 Planarity : 0.004 0.053 5303 Dihedral : 16.868 178.135 5737 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 8.27 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3565 helix: 1.18 (0.15), residues: 1255 sheet: 0.51 (0.25), residues: 458 loop : -0.97 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 259 HIS 0.012 0.001 HIS I 379 PHE 0.019 0.002 PHE A 401 TYR 0.030 0.001 TYR H 172 ARG 0.008 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 3.696 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: A 172 LEU cc_start: 0.5985 (tp) cc_final: 0.5661 (tp) REVERT: A 381 MET cc_start: 0.7186 (pmm) cc_final: 0.6905 (pmm) REVERT: A 399 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6515 (mpt180) REVERT: J 315 LEU cc_start: 0.8393 (tt) cc_final: 0.8158 (tt) outliers start: 41 outliers final: 37 residues processed: 245 average time/residue: 0.4566 time to fit residues: 177.7564 Evaluate side-chains 239 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 204 optimal weight: 0.5980 chunk 262 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 357 optimal weight: 9.9990 chunk 223 optimal weight: 0.3980 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS H 37 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32561 Z= 0.249 Angle : 0.573 10.417 44789 Z= 0.304 Chirality : 0.041 0.239 4930 Planarity : 0.005 0.053 5303 Dihedral : 16.873 177.952 5737 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.44 % Allowed : 8.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3565 helix: 1.19 (0.15), residues: 1250 sheet: 0.43 (0.25), residues: 465 loop : -1.07 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 259 HIS 0.037 0.001 HIS E 231 PHE 0.027 0.002 PHE J 287 TYR 0.022 0.001 TYR H 194 ARG 0.013 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 217 time to evaluate : 3.393 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: A 399 ARG cc_start: 0.6946 (mmt180) cc_final: 0.6534 (mpt180) REVERT: G 70 GLN cc_start: 0.4968 (pp30) cc_final: 0.4640 (pp30) REVERT: J 315 LEU cc_start: 0.8346 (tt) cc_final: 0.8139 (tt) outliers start: 44 outliers final: 36 residues processed: 246 average time/residue: 0.4666 time to fit residues: 181.8118 Evaluate side-chains 239 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 243 optimal weight: 0.0570 chunk 176 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 281 optimal weight: 10.0000 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS H 81 GLN J 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32561 Z= 0.155 Angle : 0.552 16.998 44789 Z= 0.287 Chirality : 0.039 0.234 4930 Planarity : 0.004 0.050 5303 Dihedral : 16.829 177.889 5737 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 9.06 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3565 helix: 1.32 (0.15), residues: 1252 sheet: 0.53 (0.25), residues: 460 loop : -1.03 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 259 HIS 0.013 0.001 HIS E 231 PHE 0.027 0.001 PHE I 63 TYR 0.018 0.001 TYR H 194 ARG 0.012 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ARG cc_start: 0.6960 (mmt180) cc_final: 0.6554 (mpt180) REVERT: A 403 PHE cc_start: 0.7894 (m-80) cc_final: 0.7461 (m-10) REVERT: G 70 GLN cc_start: 0.5076 (pp30) cc_final: 0.4683 (pp30) REVERT: J 315 LEU cc_start: 0.8350 (tt) cc_final: 0.8135 (tt) outliers start: 40 outliers final: 34 residues processed: 235 average time/residue: 0.4616 time to fit residues: 170.5228 Evaluate side-chains 234 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 173 GLU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 352 VAL Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 333 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 261 optimal weight: 0.4980 chunk 102 optimal weight: 0.0870 chunk 301 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32561 Z= 0.219 Angle : 0.576 14.463 44789 Z= 0.300 Chirality : 0.040 0.236 4930 Planarity : 0.004 0.054 5303 Dihedral : 16.818 179.340 5737 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.37 % Allowed : 9.35 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3565 helix: 1.30 (0.15), residues: 1251 sheet: 0.47 (0.25), residues: 461 loop : -1.09 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 259 HIS 0.027 0.001 HIS E 231 PHE 0.020 0.002 PHE J 291 TYR 0.017 0.001 TYR H 194 ARG 0.013 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.7230 (pmm) cc_final: 0.6124 (ppp) REVERT: A 399 ARG cc_start: 0.6935 (mmt180) cc_final: 0.6565 (mpt180) REVERT: G 97 MET cc_start: 0.8044 (mmm) cc_final: 0.7689 (mtt) REVERT: H 42 ILE cc_start: 0.8673 (mp) cc_final: 0.8397 (mm) REVERT: J 312 LEU cc_start: 0.8739 (pp) cc_final: 0.8485 (pt) REVERT: J 315 LEU cc_start: 0.8303 (tt) cc_final: 0.8096 (tt) outliers start: 42 outliers final: 38 residues processed: 240 average time/residue: 0.4623 time to fit residues: 176.9694 Evaluate side-chains 238 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 TRP Chi-restraints excluded: chain B residue 293 HIS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 214 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 3.9990 chunk 352 optimal weight: 0.3980 chunk 215 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 369 optimal weight: 0.7980 chunk 340 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS H 81 GLN I 97 HIS ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32561 Z= 0.154 Angle : 0.558 15.121 44789 Z= 0.289 Chirality : 0.039 0.233 4930 Planarity : 0.004 0.055 5303 Dihedral : 16.772 178.642 5737 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.18 % Allowed : 9.55 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3565 helix: 1.37 (0.15), residues: 1256 sheet: 0.58 (0.25), residues: 462 loop : -1.05 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 259 HIS 0.029 0.001 HIS E 231 PHE 0.016 0.001 PHE J 291 TYR 0.017 0.001 TYR H 194 ARG 0.014 0.000 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.7203 (pmm) cc_final: 0.6144 (ppp) REVERT: A 399 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6612 (mpt180) REVERT: G 97 MET cc_start: 0.8020 (mmm) cc_final: 0.7676 (mtt) REVERT: H 42 ILE cc_start: 0.8664 (mp) cc_final: 0.8408 (mm) REVERT: J 315 LEU cc_start: 0.8283 (tt) cc_final: 0.8075 (tt) outliers start: 36 outliers final: 33 residues processed: 241 average time/residue: 0.4700 time to fit residues: 180.1413 Evaluate side-chains 234 residues out of total 3058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 202 TRP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS H 81 GLN ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070211 restraints weight = 71547.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070483 restraints weight = 67059.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.070595 restraints weight = 53217.237| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32561 Z= 0.222 Angle : 0.586 16.835 44789 Z= 0.304 Chirality : 0.040 0.234 4930 Planarity : 0.004 0.062 5303 Dihedral : 16.784 179.922 5737 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.28 % Allowed : 9.65 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3565 helix: 1.31 (0.15), residues: 1256 sheet: 0.53 (0.25), residues: 462 loop : -1.10 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP J 259 HIS 0.014 0.001 HIS E 231 PHE 0.029 0.002 PHE I 63 TYR 0.016 0.001 TYR H 194 ARG 0.014 0.000 ARG C 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5310.82 seconds wall clock time: 98 minutes 32.31 seconds (5912.31 seconds total)