Starting phenix.real_space_refine on Fri Mar 22 11:07:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/03_2024/8oz6_17299.pdb" } resolution = 3.97 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. 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 132 5.49 5 S 96 5.16 5 C 20236 2.51 5 N 5300 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 387": "OD1" <-> "OD2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 40": "OD1" <-> "OD2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G GLU 306": "OE1" <-> "OE2" Residue "G GLU 394": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 133": "OD1" <-> "OD2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 444": "OE1" <-> "OE2" Residue "H GLU 449": "OE1" <-> "OE2" Residue "H GLU 488": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 15.98, per 1000 atoms: 0.50 Number of scatterers: 32004 At special positions: 0 Unit cell: (177.87, 208.12, 165.77, 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 96 16.00 P 132 15.00 O 6240 8.00 N 5300 7.00 C 20236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.81 Conformation dependent library (CDL) restraints added in 5.1 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 28 sheets defined 39.3% alpha, 14.3% beta 11 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 10.28 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.825A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.081A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.037A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.118A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.522A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.682A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.865A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.695A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.537A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.672A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.716A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.824A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.529A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.526A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.928A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.558A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.168A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.300A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.541A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.537A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 353 through 366 removed outlier: 3.557A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.797A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 46 through 62 removed outlier: 4.095A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.642A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.702A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.568A pdb=" N VAL D 162 " --> pdb=" O LYS D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.523A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.841A pdb=" N ALA D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.852A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.710A pdb=" N ASP D 458 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.789A pdb=" N ASP D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.718A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.626A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.838A pdb=" N PHE E 93 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 94' Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.528A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 157 removed outlier: 3.654A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.056A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.548A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.950A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 4.527A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.086A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.778A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 132 removed outlier: 4.173A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 3.549A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.692A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 218 Processing helix chain 'F' and resid 230 through 234 removed outlier: 3.750A pdb=" N ASP F 233 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.505A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.518A pdb=" N TYR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.596A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.837A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.550A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'G' and resid 10 through 13 removed outlier: 3.801A pdb=" N ASP G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.939A pdb=" N THR G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 65 through 70 removed outlier: 4.612A pdb=" N GLN G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.729A pdb=" N ILE G 108 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.913A pdb=" N GLY G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 removed outlier: 3.678A pdb=" N PHE G 158 " --> pdb=" O TYR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.684A pdb=" N ASP G 222 " --> pdb=" O TRP G 219 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR G 224 " --> pdb=" O TYR G 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 224' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.575A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 242 through 249 removed outlier: 3.519A pdb=" N ILE G 246 " --> pdb=" O PRO G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 280 removed outlier: 4.233A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 353 through 367 removed outlier: 4.180A pdb=" N ASN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.905A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.637A pdb=" N GLY H 17 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 31 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.737A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 97 through 106 Processing helix chain 'H' and resid 109 through 132 removed outlier: 4.028A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.170A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.679A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.590A pdb=" N ALA H 259 " --> pdb=" O THR H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 348 removed outlier: 3.660A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.550A pdb=" N TRP H 370 " --> pdb=" O ASN H 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.578A pdb=" N ASP H 458 " --> pdb=" O GLN H 454 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.630A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.788A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.902A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 62 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 415 removed outlier: 8.367A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3 through 6 current: chain 'B' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 316 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.583A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.513A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.671A pdb=" N THR B 92 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 305 removed outlier: 3.655A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.584A pdb=" N LYS C 4 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 172 removed outlier: 8.431A pdb=" N LEU D 4 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 411 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR D 6 " --> pdb=" O LYS C 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 6 current: chain 'D' and resid 298 through 305 removed outlier: 3.539A pdb=" N PHE D 304 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 312 " --> pdb=" O PHE D 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 315 current: chain 'D' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 389 current: chain 'D' and resid 417 through 420 Processing sheet with id=AB1, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.297A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 334 " --> pdb=" O LYS C 328 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.588A pdb=" N THR D 92 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 425 through 426 removed outlier: 3.803A pdb=" N VAL D 426 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 5.831A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 4 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 291 through 294 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 removed outlier: 8.672A pdb=" N LEU F 4 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 3 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 3.534A pdb=" N PHE F 304 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F 312 " --> pdb=" O PHE F 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 315 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AB9, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.589A pdb=" N GLN F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.328A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.921A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 32 through 33 removed outlier: 5.622A pdb=" N ILE G 5 " --> pdb=" O TRP G 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS G 4 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU G 61 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE G 6 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 63 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 8 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 165 through 178 current: chain 'G' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 291 through 294 current: chain 'G' and resid 317 through 328 removed outlier: 3.639A pdb=" N VAL G 334 " --> pdb=" O LYS G 328 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 415 removed outlier: 4.302A pdb=" N ASN G 413 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR H 6 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N SER G 415 " --> pdb=" O TYR H 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 3.527A pdb=" N PHE H 304 " --> pdb=" O VAL H 312 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 316 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 188 Processing sheet with id=AC8, first strand: chain 'G' and resid 304 through 305 Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 92 through 95 removed outlier: 7.099A pdb=" N SER H 41 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS H 94 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 43 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 999 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 11.60 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3965 1.24 - 1.38: 8709 1.38 - 1.53: 15872 1.53 - 1.67: 4370 1.67 - 1.81: 148 Bond restraints: 33064 Sorted by residual: bond pdb=" CG PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.503 1.098 0.405 3.40e-02 8.65e+02 1.42e+02 bond pdb=" CG PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO F 158 " pdb=" CD PRO F 158 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+02 bond pdb=" CG PRO D 500 " pdb=" CD PRO D 500 " ideal model delta sigma weight residual 1.503 1.305 0.198 3.40e-02 8.65e+02 3.40e+01 bond pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.14e+01 ... (remaining 33059 not shown) Histogram of bond angle deviations from ideal: 81.54 - 93.14: 7 93.14 - 104.75: 973 104.75 - 116.35: 21948 116.35 - 127.95: 21920 127.95 - 139.55: 408 Bond angle restraints: 45256 Sorted by residual: angle pdb=" N PRO D 378 " pdb=" CD PRO D 378 " pdb=" CG PRO D 378 " ideal model delta sigma weight residual 103.20 81.54 21.66 1.50e+00 4.44e-01 2.08e+02 angle pdb=" N PRO D 76 " pdb=" CD PRO D 76 " pdb=" CG PRO D 76 " ideal model delta sigma weight residual 103.20 82.69 20.51 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO F 158 " pdb=" CD PRO F 158 " pdb=" CG PRO F 158 " ideal model delta sigma weight residual 103.20 83.55 19.65 1.50e+00 4.44e-01 1.72e+02 angle pdb=" CA PRO D 378 " pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 112.00 98.26 13.74 1.40e+00 5.10e-01 9.64e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 ... (remaining 45251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 19247 35.69 - 71.37: 645 71.37 - 107.06: 33 107.06 - 142.74: 8 142.74 - 178.43: 7 Dihedral angle restraints: 19940 sinusoidal: 9432 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 21.57 178.43 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 9 " pdb=" C1' U M 9 " pdb=" N1 U M 9 " pdb=" C2 U M 9 " ideal model delta sinusoidal sigma weight residual -160.00 -7.26 -152.74 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 48.79 151.21 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 19937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3585 0.038 - 0.076: 1001 0.076 - 0.114: 312 0.114 - 0.152: 64 0.152 - 0.190: 6 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA PRO D 427 " pdb=" N PRO D 427 " pdb=" C PRO D 427 " pdb=" CB PRO D 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TYR D 56 " pdb=" N TYR D 56 " pdb=" C TYR D 56 " pdb=" CB TYR D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4965 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 499 " -0.065 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 500 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 254 " -0.019 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" CG TRP D 254 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP D 254 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 254 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 157 " -0.063 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 158 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " -0.048 5.00e-02 4.00e+02 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 631 2.65 - 3.22: 30314 3.22 - 3.78: 52738 3.78 - 4.34: 73379 4.34 - 4.90: 112902 Nonbonded interactions: 269964 Sorted by model distance: nonbonded pdb=" OG SER C 354 " pdb=" O2' U K 8 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR A 416 " pdb=" O THR B 404 " model vdw 2.122 2.440 nonbonded pdb=" OD1 ASN A 151 " pdb=" NE2 GLN A 155 " model vdw 2.131 2.520 nonbonded pdb=" OH TYR C 190 " pdb=" O ALA C 220 " model vdw 2.134 2.440 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.140 2.440 ... (remaining 269959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.030 Extract box with map and model: 7.450 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 87.030 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.280 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 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 : 0.005 0.405 33064 Z= 0.312 Angle : 0.734 21.656 45256 Z= 0.433 Chirality : 0.040 0.190 4968 Planarity : 0.005 0.091 5236 Dihedral : 16.726 178.426 13148 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.95 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.11 (0.15), residues: 1190 sheet: -1.09 (0.21), residues: 612 loop : -1.13 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 254 HIS 0.007 0.001 HIS E 358 PHE 0.031 0.002 PHE E 135 TYR 0.035 0.001 TYR D 56 ARG 0.008 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.7500 (mt) cc_final: 0.7210 (mm) REVERT: A 156 GLN cc_start: 0.7743 (mt0) cc_final: 0.7165 (mp10) REVERT: A 210 TYR cc_start: 0.7786 (t80) cc_final: 0.7569 (t80) REVERT: B 118 VAL cc_start: 0.7046 (t) cc_final: 0.6820 (t) REVERT: B 478 VAL cc_start: 0.7524 (p) cc_final: 0.7262 (m) REVERT: C 122 MET cc_start: 0.6943 (tmm) cc_final: 0.6714 (tmm) REVERT: C 162 LYS cc_start: 0.6753 (mptt) cc_final: 0.5963 (mmmt) REVERT: D 290 LYS cc_start: 0.7512 (tptt) cc_final: 0.7130 (tptp) REVERT: E 287 MET cc_start: 0.3500 (tmm) cc_final: 0.3217 (tmm) REVERT: E 305 PHE cc_start: 0.8034 (t80) cc_final: 0.7646 (t80) REVERT: F 390 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6937 (tmtt) REVERT: G 62 LEU cc_start: 0.8220 (tp) cc_final: 0.7976 (tp) REVERT: G 192 TRP cc_start: 0.6359 (p-90) cc_final: 0.5188 (t60) REVERT: G 193 MET cc_start: 0.5917 (mpp) cc_final: 0.3739 (mtt) REVERT: G 393 LEU cc_start: 0.8649 (mt) cc_final: 0.8302 (tp) REVERT: H 86 TRP cc_start: 0.6116 (t60) cc_final: 0.5134 (t60) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.4217 time to fit residues: 286.6362 Evaluate side-chains 276 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 0.0070 chunk 184 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 282 optimal weight: 0.0050 chunk 109 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 overall best weight: 1.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS E 116 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 ASN G 109 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33064 Z= 0.192 Angle : 0.617 9.154 45256 Z= 0.323 Chirality : 0.042 0.222 4968 Planarity : 0.005 0.058 5236 Dihedral : 17.217 160.856 5860 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.10 % Favored : 94.59 % Rotamer: Outliers : 1.31 % Allowed : 8.51 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.95 (0.14), residues: 3532 helix: 0.34 (0.15), residues: 1202 sheet: -1.06 (0.21), residues: 626 loop : -1.11 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 254 HIS 0.008 0.001 HIS D 251 PHE 0.026 0.002 PHE D 210 TYR 0.019 0.001 TYR D 56 ARG 0.008 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 331 time to evaluate : 3.439 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: A 14 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: A 210 TYR cc_start: 0.7771 (t80) cc_final: 0.7548 (t80) REVERT: A 336 MET cc_start: 0.4804 (mmp) cc_final: 0.3524 (tpp) REVERT: B 118 VAL cc_start: 0.7162 (t) cc_final: 0.6956 (t) REVERT: C 1 MET cc_start: 0.7117 (pmm) cc_final: 0.6759 (pmm) REVERT: C 122 MET cc_start: 0.7321 (tmm) cc_final: 0.6968 (tmm) REVERT: C 128 LEU cc_start: 0.8613 (mt) cc_final: 0.8040 (tp) REVERT: C 162 LYS cc_start: 0.6666 (mptt) cc_final: 0.5978 (mmmt) REVERT: C 410 PHE cc_start: 0.5750 (m-10) cc_final: 0.5345 (m-80) REVERT: D 290 LYS cc_start: 0.7475 (tptt) cc_final: 0.7093 (tptp) REVERT: D 435 MET cc_start: -0.0450 (ttp) cc_final: -0.0684 (ttp) REVERT: E 141 PRO cc_start: 0.3452 (Cg_exo) cc_final: 0.3140 (Cg_endo) REVERT: E 305 PHE cc_start: 0.8114 (t80) cc_final: 0.7761 (t80) REVERT: F 37 TYR cc_start: 0.3881 (m-80) cc_final: 0.3454 (m-80) REVERT: F 435 MET cc_start: 0.6186 (mmm) cc_final: 0.5774 (mmm) REVERT: G 192 TRP cc_start: 0.6227 (p-90) cc_final: 0.4969 (t60) REVERT: G 193 MET cc_start: 0.4860 (mpp) cc_final: 0.4106 (mtt) REVERT: G 393 LEU cc_start: 0.8532 (mt) cc_final: 0.8322 (tp) REVERT: H 75 PHE cc_start: 0.7629 (t80) cc_final: 0.7369 (t80) REVERT: H 86 TRP cc_start: 0.6134 (t60) cc_final: 0.5795 (t60) REVERT: H 303 MET cc_start: 0.5399 (ttm) cc_final: 0.4924 (ttt) outliers start: 42 outliers final: 25 residues processed: 346 average time/residue: 0.4321 time to fit residues: 244.1239 Evaluate side-chains 290 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 chunk 353 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 409 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN F 439 ASN G 102 GLN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33064 Z= 0.285 Angle : 0.695 12.476 45256 Z= 0.365 Chirality : 0.043 0.193 4968 Planarity : 0.005 0.059 5236 Dihedral : 17.531 162.536 5860 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.97 % Favored : 93.71 % Rotamer: Outliers : 2.53 % Allowed : 11.23 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.25 (0.15), residues: 1212 sheet: -1.33 (0.21), residues: 586 loop : -1.16 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 254 HIS 0.008 0.001 HIS G 358 PHE 0.035 0.002 PHE H 373 TYR 0.028 0.002 TYR H 106 ARG 0.011 0.001 ARG C 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 280 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7729 (t80) cc_final: 0.7519 (t80) REVERT: A 268 LEU cc_start: 0.7808 (mm) cc_final: 0.7440 (mm) REVERT: B 118 VAL cc_start: 0.7280 (t) cc_final: 0.7062 (t) REVERT: C 1 MET cc_start: 0.7140 (pmm) cc_final: 0.6595 (pmm) REVERT: C 122 MET cc_start: 0.7574 (tmm) cc_final: 0.7327 (tmm) REVERT: C 162 LYS cc_start: 0.6827 (mptt) cc_final: 0.6136 (mmmt) REVERT: C 410 PHE cc_start: 0.5926 (m-10) cc_final: 0.5609 (m-80) REVERT: D 290 LYS cc_start: 0.7763 (tptt) cc_final: 0.7500 (tptp) REVERT: E 175 TRP cc_start: 0.4652 (m-10) cc_final: 0.4267 (m-10) REVERT: E 287 MET cc_start: 0.4542 (tmm) cc_final: 0.4222 (tmm) REVERT: F 81 VAL cc_start: 0.7645 (m) cc_final: 0.7350 (p) REVERT: F 435 MET cc_start: 0.6250 (mmm) cc_final: 0.5983 (mmm) REVERT: G 393 LEU cc_start: 0.8653 (mt) cc_final: 0.8435 (tp) REVERT: H 36 LEU cc_start: 0.6691 (tt) cc_final: 0.6485 (tt) REVERT: H 86 TRP cc_start: 0.6603 (t60) cc_final: 0.5789 (t60) REVERT: H 106 TYR cc_start: 0.4240 (m-80) cc_final: 0.3806 (m-80) REVERT: H 303 MET cc_start: 0.4648 (ttm) cc_final: 0.4367 (ttm) REVERT: H 435 MET cc_start: 0.4808 (tmm) cc_final: 0.0458 (ptp) REVERT: H 504 LYS cc_start: 0.7326 (mtmt) cc_final: 0.6672 (mtmm) outliers start: 81 outliers final: 50 residues processed: 330 average time/residue: 0.4237 time to fit residues: 230.0978 Evaluate side-chains 302 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.5980 chunk 246 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33064 Z= 0.217 Angle : 0.623 11.666 45256 Z= 0.326 Chirality : 0.041 0.158 4968 Planarity : 0.005 0.059 5236 Dihedral : 17.556 163.161 5860 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.72 % Favored : 93.97 % Rotamer: Outliers : 2.25 % Allowed : 13.67 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.99 (0.14), residues: 3532 helix: 0.42 (0.15), residues: 1224 sheet: -1.36 (0.21), residues: 580 loop : -1.14 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 254 HIS 0.010 0.001 HIS G 358 PHE 0.039 0.002 PHE H 373 TYR 0.020 0.001 TYR F 37 ARG 0.015 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 3.794 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 268 LEU cc_start: 0.7742 (mm) cc_final: 0.7391 (mm) REVERT: B 7 ILE cc_start: 0.8030 (pt) cc_final: 0.7509 (mp) REVERT: B 118 VAL cc_start: 0.7130 (t) cc_final: 0.6875 (t) REVERT: C 122 MET cc_start: 0.7450 (tmm) cc_final: 0.7066 (tmm) REVERT: C 388 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6891 (p0) REVERT: C 410 PHE cc_start: 0.5981 (m-10) cc_final: 0.5556 (m-80) REVERT: D 290 LYS cc_start: 0.7719 (tptt) cc_final: 0.7030 (tptp) REVERT: E 257 ARG cc_start: 0.6432 (tpt90) cc_final: 0.6023 (tpt90) REVERT: F 81 VAL cc_start: 0.7543 (m) cc_final: 0.7146 (p) REVERT: G 391 PHE cc_start: 0.8222 (p90) cc_final: 0.7999 (p90) REVERT: H 86 TRP cc_start: 0.6258 (t60) cc_final: 0.5812 (t60) REVERT: H 489 ILE cc_start: 0.6526 (tp) cc_final: 0.6289 (tp) outliers start: 72 outliers final: 51 residues processed: 336 average time/residue: 0.4016 time to fit residues: 223.1185 Evaluate side-chains 312 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 260 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 0.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 296 ASN ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33064 Z= 0.267 Angle : 0.675 10.278 45256 Z= 0.355 Chirality : 0.043 0.180 4968 Planarity : 0.005 0.061 5236 Dihedral : 17.715 164.155 5860 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 25.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.51 % Favored : 93.18 % Rotamer: Outliers : 3.16 % Allowed : 14.92 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3532 helix: 0.29 (0.15), residues: 1226 sheet: -1.61 (0.20), residues: 592 loop : -1.19 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 PHE 0.037 0.002 PHE H 373 TYR 0.026 0.002 TYR H 106 ARG 0.013 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 284 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7745 (mm) cc_final: 0.7378 (mm) REVERT: B 7 ILE cc_start: 0.8034 (pt) cc_final: 0.7672 (mp) REVERT: B 118 VAL cc_start: 0.7185 (t) cc_final: 0.6937 (t) REVERT: C 122 MET cc_start: 0.7415 (tmm) cc_final: 0.7061 (tmm) REVERT: C 146 ASP cc_start: 0.4116 (OUTLIER) cc_final: 0.2021 (t0) REVERT: C 388 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7425 (p0) REVERT: C 410 PHE cc_start: 0.5831 (m-10) cc_final: 0.5388 (m-80) REVERT: D 290 LYS cc_start: 0.7832 (tptt) cc_final: 0.7144 (tptp) REVERT: E 175 TRP cc_start: 0.4873 (m-10) cc_final: 0.4376 (m-10) REVERT: E 193 MET cc_start: 0.4710 (ptp) cc_final: 0.4509 (ptt) REVERT: E 336 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6331 (mtm) REVERT: F 81 VAL cc_start: 0.7485 (m) cc_final: 0.7152 (p) REVERT: G 133 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8621 (pt0) REVERT: G 273 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.5332 (t80) REVERT: H 86 TRP cc_start: 0.6441 (t60) cc_final: 0.5819 (t60) REVERT: H 106 TYR cc_start: 0.3999 (m-80) cc_final: 0.3318 (m-80) REVERT: H 243 ARG cc_start: 0.5421 (mtp180) cc_final: 0.3998 (ptp90) REVERT: H 435 MET cc_start: 0.4954 (tmm) cc_final: 0.0728 (ptp) outliers start: 101 outliers final: 71 residues processed: 349 average time/residue: 0.4103 time to fit residues: 236.1527 Evaluate side-chains 336 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 261 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 398 LYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN H 302 GLN ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 33064 Z= 0.291 Angle : 0.694 15.852 45256 Z= 0.364 Chirality : 0.044 0.208 4968 Planarity : 0.005 0.060 5236 Dihedral : 17.825 165.385 5860 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.85 % Favored : 92.87 % Rotamer: Outliers : 3.75 % Allowed : 15.64 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3532 helix: 0.12 (0.14), residues: 1230 sheet: -1.73 (0.21), residues: 558 loop : -1.37 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 254 HIS 0.010 0.001 HIS G 358 PHE 0.032 0.002 PHE H 373 TYR 0.030 0.002 TYR H 106 ARG 0.009 0.001 ARG E 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 272 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: A 268 LEU cc_start: 0.7686 (mm) cc_final: 0.7324 (mm) REVERT: B 118 VAL cc_start: 0.7242 (t) cc_final: 0.7010 (t) REVERT: B 219 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6354 (mt) REVERT: B 271 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5446 (mt) REVERT: C 122 MET cc_start: 0.7341 (tmm) cc_final: 0.6934 (tmm) REVERT: C 204 THR cc_start: 0.7358 (t) cc_final: 0.6915 (t) REVERT: C 388 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7439 (p0) REVERT: C 410 PHE cc_start: 0.5823 (m-10) cc_final: 0.5547 (m-80) REVERT: D 290 LYS cc_start: 0.7773 (tptt) cc_final: 0.7084 (tptp) REVERT: E 175 TRP cc_start: 0.4897 (m-10) cc_final: 0.4555 (m-10) REVERT: E 336 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6578 (mtm) REVERT: F 101 ILE cc_start: 0.5548 (pp) cc_final: 0.5324 (pp) REVERT: G 133 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8566 (pt0) REVERT: G 287 MET cc_start: -0.0414 (tpt) cc_final: -0.0674 (tpt) REVERT: H 161 MET cc_start: 0.2653 (tmm) cc_final: -0.0263 (mtm) REVERT: H 243 ARG cc_start: 0.5611 (mtp180) cc_final: 0.4146 (ptp90) REVERT: H 435 MET cc_start: 0.4702 (tmm) cc_final: 0.0459 (ptp) outliers start: 120 outliers final: 83 residues processed: 353 average time/residue: 0.4042 time to fit residues: 234.2337 Evaluate side-chains 337 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 250 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 346 optimal weight: 0.0870 chunk 217 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33064 Z= 0.202 Angle : 0.633 12.593 45256 Z= 0.329 Chirality : 0.042 0.242 4968 Planarity : 0.004 0.060 5236 Dihedral : 17.751 166.737 5860 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.29 % Favored : 93.49 % Rotamer: Outliers : 2.72 % Allowed : 17.08 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3532 helix: 0.44 (0.15), residues: 1218 sheet: -1.56 (0.21), residues: 560 loop : -1.29 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 254 HIS 0.010 0.001 HIS G 358 PHE 0.030 0.002 PHE A 17 TYR 0.026 0.001 TYR H 346 ARG 0.009 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 285 time to evaluate : 3.455 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 268 LEU cc_start: 0.7774 (mm) cc_final: 0.7523 (mm) REVERT: B 7 ILE cc_start: 0.8017 (pt) cc_final: 0.7500 (mp) REVERT: B 118 VAL cc_start: 0.7130 (t) cc_final: 0.6885 (t) REVERT: B 219 ILE cc_start: 0.7127 (mt) cc_final: 0.6566 (mt) REVERT: B 303 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6601 (ttm) REVERT: B 503 PHE cc_start: 0.6612 (m-10) cc_final: 0.6098 (m-80) REVERT: C 122 MET cc_start: 0.7155 (tmm) cc_final: 0.6653 (tmm) REVERT: C 388 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7341 (p0) REVERT: C 410 PHE cc_start: 0.5993 (m-10) cc_final: 0.5507 (m-80) REVERT: C 411 LYS cc_start: 0.6933 (pttm) cc_final: 0.6575 (pttm) REVERT: D 290 LYS cc_start: 0.7870 (tptt) cc_final: 0.7207 (tptp) REVERT: D 398 LYS cc_start: 0.6627 (pttm) cc_final: 0.6300 (tmmt) REVERT: E 336 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5987 (mtm) REVERT: F 101 ILE cc_start: 0.5427 (pp) cc_final: 0.5223 (pp) REVERT: G 133 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8598 (pt0) REVERT: G 146 ASP cc_start: 0.0905 (OUTLIER) cc_final: -0.0273 (m-30) REVERT: G 287 MET cc_start: -0.0755 (tpt) cc_final: -0.1002 (tpt) REVERT: H 36 LEU cc_start: 0.6840 (tt) cc_final: 0.6561 (mm) REVERT: H 161 MET cc_start: 0.2301 (tmm) cc_final: 0.2094 (tmm) REVERT: H 243 ARG cc_start: 0.5850 (mtp180) cc_final: 0.4446 (ptp90) outliers start: 87 outliers final: 65 residues processed: 341 average time/residue: 0.4158 time to fit residues: 233.5303 Evaluate side-chains 327 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 258 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 0.5980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33064 Z= 0.254 Angle : 0.686 13.895 45256 Z= 0.356 Chirality : 0.044 0.246 4968 Planarity : 0.005 0.064 5236 Dihedral : 17.810 167.582 5860 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 3.47 % Allowed : 16.86 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3532 helix: 0.25 (0.15), residues: 1222 sheet: -1.69 (0.21), residues: 554 loop : -1.37 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 PHE 0.028 0.002 PHE H 373 TYR 0.038 0.002 TYR H 106 ARG 0.010 0.001 ARG E 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 257 time to evaluate : 3.184 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: A 268 LEU cc_start: 0.7844 (mm) cc_final: 0.7494 (mm) REVERT: B 7 ILE cc_start: 0.8119 (pt) cc_final: 0.7630 (mp) REVERT: B 118 VAL cc_start: 0.7333 (t) cc_final: 0.7117 (t) REVERT: B 219 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6412 (mt) REVERT: C 122 MET cc_start: 0.7290 (tmm) cc_final: 0.6854 (tmm) REVERT: C 388 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7381 (p0) REVERT: C 410 PHE cc_start: 0.6036 (m-10) cc_final: 0.5521 (m-80) REVERT: C 411 LYS cc_start: 0.7062 (pttm) cc_final: 0.6771 (pttm) REVERT: D 290 LYS cc_start: 0.8052 (tptt) cc_final: 0.7416 (tptp) REVERT: D 398 LYS cc_start: 0.6647 (pttm) cc_final: 0.6406 (tmmt) REVERT: D 447 LYS cc_start: 0.4609 (OUTLIER) cc_final: 0.3100 (mmtp) REVERT: E 309 MET cc_start: 0.5809 (tpt) cc_final: 0.5557 (tpt) REVERT: E 336 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.5820 (mtm) REVERT: F 101 ILE cc_start: 0.5390 (pp) cc_final: 0.5179 (pp) REVERT: F 353 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: G 133 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8595 (pt0) REVERT: G 146 ASP cc_start: 0.1188 (OUTLIER) cc_final: 0.0034 (m-30) REVERT: G 287 MET cc_start: -0.1045 (tpt) cc_final: -0.1364 (tpt) REVERT: G 336 MET cc_start: 0.2903 (OUTLIER) cc_final: 0.2438 (mmt) REVERT: H 86 TRP cc_start: 0.4536 (t60) cc_final: 0.4274 (t60) REVERT: H 243 ARG cc_start: 0.5938 (mtp180) cc_final: 0.4498 (ptp90) outliers start: 111 outliers final: 81 residues processed: 335 average time/residue: 0.4175 time to fit residues: 229.2718 Evaluate side-chains 331 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 243 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 506 TYR Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 216 THR Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 323 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 292 optimal weight: 0.8980 chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33064 Z= 0.217 Angle : 0.665 13.630 45256 Z= 0.342 Chirality : 0.043 0.252 4968 Planarity : 0.005 0.059 5236 Dihedral : 17.818 169.884 5860 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.48 % Favored : 93.32 % Rotamer: Outliers : 3.00 % Allowed : 17.55 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3532 helix: 0.42 (0.15), residues: 1214 sheet: -1.67 (0.21), residues: 550 loop : -1.35 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 PHE 0.032 0.002 PHE H 373 TYR 0.020 0.001 TYR D 56 ARG 0.010 0.001 ARG E 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 270 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7783 (mm) cc_final: 0.7563 (mm) REVERT: B 118 VAL cc_start: 0.7217 (t) cc_final: 0.6971 (t) REVERT: B 219 ILE cc_start: 0.6889 (mt) cc_final: 0.6338 (mt) REVERT: B 303 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6390 (mtp) REVERT: B 482 PHE cc_start: 0.5753 (m-10) cc_final: 0.5331 (m-10) REVERT: B 503 PHE cc_start: 0.6680 (m-10) cc_final: 0.6214 (m-80) REVERT: C 122 MET cc_start: 0.7065 (tmm) cc_final: 0.6583 (tmm) REVERT: C 410 PHE cc_start: 0.5928 (m-10) cc_final: 0.5411 (m-80) REVERT: C 411 LYS cc_start: 0.7104 (pttm) cc_final: 0.6790 (pttm) REVERT: D 74 MET cc_start: 0.4851 (tmm) cc_final: 0.4638 (tmm) REVERT: D 398 LYS cc_start: 0.6613 (pttm) cc_final: 0.6376 (tmmt) REVERT: D 447 LYS cc_start: 0.4128 (OUTLIER) cc_final: 0.3019 (mmtp) REVERT: E 309 MET cc_start: 0.5652 (tpt) cc_final: 0.5409 (tpt) REVERT: E 321 PHE cc_start: -0.0731 (OUTLIER) cc_final: -0.1018 (t80) REVERT: E 336 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5714 (mtm) REVERT: F 70 ILE cc_start: 0.7881 (mm) cc_final: 0.7601 (tt) REVERT: F 74 MET cc_start: 0.2039 (ptt) cc_final: 0.1791 (ptp) REVERT: F 353 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5879 (m-10) REVERT: G 133 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8666 (pt0) REVERT: G 146 ASP cc_start: 0.1309 (OUTLIER) cc_final: 0.0194 (m-30) REVERT: G 287 MET cc_start: -0.1257 (tpt) cc_final: -0.1500 (tpt) REVERT: G 336 MET cc_start: 0.3093 (OUTLIER) cc_final: 0.2611 (mmt) outliers start: 96 outliers final: 74 residues processed: 337 average time/residue: 0.4275 time to fit residues: 236.4030 Evaluate side-chains 326 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 245 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 4.9990 chunk 341 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33064 Z= 0.299 Angle : 0.736 13.970 45256 Z= 0.384 Chirality : 0.045 0.415 4968 Planarity : 0.005 0.059 5236 Dihedral : 18.000 170.520 5860 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 29.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.30 % Favored : 91.51 % Rotamer: Outliers : 2.88 % Allowed : 18.05 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3532 helix: 0.10 (0.15), residues: 1220 sheet: -1.75 (0.21), residues: 566 loop : -1.46 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP D 254 HIS 0.009 0.001 HIS G 358 PHE 0.047 0.002 PHE C 17 TYR 0.026 0.002 TYR H 346 ARG 0.013 0.001 ARG E 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 247 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7859 (mm) cc_final: 0.7550 (mm) REVERT: B 118 VAL cc_start: 0.7352 (t) cc_final: 0.7134 (t) REVERT: B 219 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.6845 (mt) REVERT: B 303 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6460 (mtm) REVERT: B 482 PHE cc_start: 0.5756 (m-10) cc_final: 0.5452 (m-10) REVERT: B 503 PHE cc_start: 0.6695 (m-10) cc_final: 0.6423 (m-80) REVERT: C 122 MET cc_start: 0.7189 (tmm) cc_final: 0.6753 (tmm) REVERT: C 410 PHE cc_start: 0.5866 (m-10) cc_final: 0.5411 (m-80) REVERT: C 411 LYS cc_start: 0.7126 (pttm) cc_final: 0.6795 (pttm) REVERT: E 309 MET cc_start: 0.6093 (tpt) cc_final: 0.5817 (tpt) REVERT: E 321 PHE cc_start: -0.0402 (OUTLIER) cc_final: -0.0804 (t80) REVERT: F 70 ILE cc_start: 0.7849 (mm) cc_final: 0.7591 (tt) REVERT: F 353 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6110 (m-10) REVERT: G 146 ASP cc_start: 0.1469 (OUTLIER) cc_final: 0.0386 (m-30) REVERT: G 287 MET cc_start: -0.1650 (tpt) cc_final: -0.1992 (tpt) REVERT: G 336 MET cc_start: 0.3060 (OUTLIER) cc_final: 0.2615 (mmt) REVERT: H 443 ILE cc_start: 0.9160 (mp) cc_final: 0.8919 (pt) outliers start: 92 outliers final: 81 residues processed: 316 average time/residue: 0.4182 time to fit residues: 215.0992 Evaluate side-chains 327 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 240 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 299 CYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 506 TYR Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 426 VAL Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 0.0060 chunk 263 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 2.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN C 151 ASN D 322 ASN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.103929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.088287 restraints weight = 204416.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.089692 restraints weight = 146618.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.090665 restraints weight = 115775.960| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33064 Z= 0.205 Angle : 0.674 14.324 45256 Z= 0.345 Chirality : 0.043 0.278 4968 Planarity : 0.004 0.059 5236 Dihedral : 17.950 173.419 5860 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 2.66 % Allowed : 18.30 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3532 helix: 0.38 (0.15), residues: 1214 sheet: -1.65 (0.22), residues: 522 loop : -1.43 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 254 HIS 0.010 0.001 HIS G 358 PHE 0.050 0.002 PHE C 17 TYR 0.047 0.001 TYR D 321 ARG 0.009 0.001 ARG E 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5792.87 seconds wall clock time: 107 minutes 38.94 seconds (6458.94 seconds total)