Starting phenix.real_space_refine on Mon Apr 15 01:09:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozg_17308/04_2024/8ozg_17308_updated.pdb" } resolution = 3.37 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= 0.030 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: 6 Type Number sf(0) Gaussians P 136 5.49 5 Mg 1 5.21 5 S 96 5.16 5 C 20266 2.51 5 N 5310 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 233": "OD1" <-> "OD2" Residue "E ASP 273": "OD1" <-> "OD2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 449": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 44": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "F ASP 172": "OD1" <-> "OD2" Residue "F PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "G PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 133": "OD1" <-> "OD2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G ASP 203": "OD1" <-> "OD2" Residue "G PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 273": "OD1" <-> "OD2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 400": "OE1" <-> "OE2" Residue "H ASP 119": "OD1" <-> "OD2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 286": "OE1" <-> "OE2" Residue "H TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 301": "OE1" <-> "OE2" Residue "H PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 406": "OE1" <-> "OE2" Residue "H TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 3": "OE1" <-> "OE2" Residue "M TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 55": "OD1" <-> "OD2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M GLU 316": "OE1" <-> "OE2" Residue "M TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 380": "OE1" <-> "OE2" Residue "M TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 436": "OE1" <-> "OE2" Residue "M GLU 449": "OE1" <-> "OE2" Residue "M GLU 476": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32077 Number of models: 1 Model: "" Number of chains: 18 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: "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: "E" 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: "F" 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: "G" 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: "H" 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: "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: "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: "M" 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: "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: 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: "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} Chain: "Q" 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MG': 1, 'AR6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.22, per 1000 atoms: 0.51 Number of scatterers: 32077 At special positions: 0 Unit cell: (177.87, 208.12, 166.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 136 15.00 Mg 1 11.99 O 6268 8.00 N 5310 7.00 C 20266 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: 12.11 Conformation dependent library (CDL) restraints added in 5.0 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... running ksdssp... Secondary structure from input PDB file: 132 helices and 37 sheets defined 33.8% alpha, 13.9% beta 21 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 14.00 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.783A pdb=" N TRP A 46 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 49 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.750A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 258 through 279 removed outlier: 4.021A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 354 through 367 removed outlier: 4.689A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.980A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.799A 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 24 through 30 Processing helix chain 'B' and resid 47 through 61 removed outlier: 4.012A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.604A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.639A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.777A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.583A pdb=" N TYR B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.524A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.779A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.746A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 72 through 88 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 228 through 232 removed outlier: 4.224A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 266 through 279 Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 354 through 367 removed outlier: 4.970A pdb=" N ASN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 383 removed outlier: 3.883A pdb=" N THR C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 47 through 61 removed outlier: 3.618A pdb=" N LYS E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.637A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.673A pdb=" N LYS E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 206 through 213 Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 249 through 263 Processing helix chain 'E' and resid 332 through 350 removed outlier: 3.993A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 376 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 452 through 464 removed outlier: 3.865A pdb=" N SER E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 490 Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'F' and resid 15 through 28 Processing helix chain 'F' and resid 43 through 55 removed outlier: 3.941A pdb=" N TRP F 46 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 49 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 72 through 88 Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 220 through 223 removed outlier: 4.429A pdb=" N PHE F 223 " --> pdb=" O ALA F 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 228 through 232 removed outlier: 4.055A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 228 through 232' Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 258 through 279 removed outlier: 4.163A pdb=" N ILE F 265 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 354 through 367 removed outlier: 4.814A pdb=" N ASN F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 384 removed outlier: 3.789A pdb=" N THR F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 24 through 30 Processing helix chain 'G' and resid 47 through 61 removed outlier: 3.811A pdb=" N LYS G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 98 through 105 removed outlier: 3.852A pdb=" N PHE G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 105 " --> pdb=" O ILE G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 130 removed outlier: 3.760A pdb=" N LYS G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'G' and resid 206 through 213 Processing helix chain 'G' and resid 231 through 233 No H-bonds generated for 'chain 'G' and resid 231 through 233' Processing helix chain 'G' and resid 249 through 264 removed outlier: 3.666A pdb=" N ALA G 259 " --> pdb=" O THR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 350 removed outlier: 4.189A pdb=" N GLN G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 376 removed outlier: 3.649A pdb=" N VAL G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 452 through 464 removed outlier: 3.798A pdb=" N LEU G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 490 removed outlier: 3.828A pdb=" N ASP G 484 " --> pdb=" O LEU G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'H' and resid 15 through 27 Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'H' and resid 110 through 113 No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 124 through 138 removed outlier: 3.597A pdb=" N LEU H 128 " --> pdb=" O TRP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 157 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 220 through 223 removed outlier: 4.290A pdb=" N PHE H 223 " --> pdb=" O ALA H 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 223' Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'H' and resid 243 through 248 Processing helix chain 'H' and resid 258 through 279 removed outlier: 4.052A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 365 Processing helix chain 'H' and resid 370 through 383 removed outlier: 4.042A pdb=" N THR H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 23 through 30 Processing helix chain 'M' and resid 47 through 61 removed outlier: 3.930A pdb=" N LYS M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE M 52 " --> pdb=" O GLN M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 81 No H-bonds generated for 'chain 'M' and resid 78 through 81' Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.538A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 105 " --> pdb=" O ILE M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 131 removed outlier: 3.646A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 149 Processing helix chain 'M' and resid 206 through 213 Processing helix chain 'M' and resid 215 through 217 No H-bonds generated for 'chain 'M' and resid 215 through 217' Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'M' and resid 332 through 350 removed outlier: 3.990A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 removed outlier: 3.553A pdb=" N ALA M 372 " --> pdb=" O GLN M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 429 No H-bonds generated for 'chain 'M' and resid 427 through 429' Processing helix chain 'M' and resid 452 through 464 removed outlier: 3.815A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER M 461 " --> pdb=" O LYS M 457 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS M 464 " --> pdb=" O LEU M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 490 removed outlier: 3.711A pdb=" N ASP M 484 " --> pdb=" O LEU M 480 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 505 No H-bonds generated for 'chain 'M' and resid 503 through 505' Processing sheet with id= A, first strand: chain 'A' and resid 117 through 119 removed outlier: 8.219A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 8 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N SER A 64 " --> pdb=" O SER A 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.715A pdb=" N TYR A 171 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 410 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= E, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 390 through 394 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 95 removed outlier: 5.837A pdb=" N VAL B 138 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE B 44 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE B 140 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 282 through 286 removed outlier: 3.792A pdb=" N ALA B 300 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 359 through 361 removed outlier: 6.986A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 419 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 117 through 119 removed outlier: 8.097A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER C 64 " --> pdb=" O SER C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= L, first strand: chain 'C' and resid 175 through 177 Processing sheet with id= M, first strand: chain 'C' and resid 186 through 188 Processing sheet with id= N, first strand: chain 'C' and resid 283 through 286 Processing sheet with id= O, first strand: chain 'C' and resid 390 through 394 Processing sheet with id= P, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.470A pdb=" N VAL E 138 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE E 44 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE E 140 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= R, first strand: chain 'E' and resid 356 through 361 removed outlier: 6.395A pdb=" N ASN E 382 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE E 359 " --> pdb=" O ASN E 382 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 384 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 361 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 386 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR E 387 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE E 445 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER E 389 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE E 443 " --> pdb=" O SER E 389 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 31 through 33 removed outlier: 7.494A pdb=" N PHE F 6 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE F 60 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N SER F 8 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU F 62 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 169 through 172 Processing sheet with id= U, first strand: chain 'F' and resid 175 through 177 Processing sheet with id= V, first strand: chain 'F' and resid 186 through 188 Processing sheet with id= W, first strand: chain 'F' and resid 283 through 286 Processing sheet with id= X, first strand: chain 'F' and resid 390 through 394 Processing sheet with id= Y, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.238A pdb=" N VAL G 138 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE G 44 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE G 140 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL G 141 " --> pdb=" O GLN G 222 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 284 through 286 Processing sheet with id= AA, first strand: chain 'G' and resid 300 through 305 removed outlier: 3.536A pdb=" N ALA G 300 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 356 through 361 removed outlier: 6.472A pdb=" N ASN G 382 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE G 359 " --> pdb=" O ASN G 382 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 384 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA G 361 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL G 386 " --> pdb=" O ALA G 361 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE G 443 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE G 419 " --> pdb=" O VAL G 412 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL G 412 " --> pdb=" O PHE G 419 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 94 through 98 removed outlier: 8.709A pdb=" N ILE H 95 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE H 60 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU H 97 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU H 62 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS H 4 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE H 60 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE H 6 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU H 62 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER H 8 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N SER H 64 " --> pdb=" O SER H 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 169 through 172 Processing sheet with id= AE, first strand: chain 'H' and resid 175 through 177 Processing sheet with id= AF, first strand: chain 'H' and resid 186 through 188 Processing sheet with id= AG, first strand: chain 'H' and resid 283 through 286 Processing sheet with id= AH, first strand: chain 'H' and resid 390 through 394 Processing sheet with id= AI, first strand: chain 'M' and resid 92 through 95 removed outlier: 6.461A pdb=" N VAL M 138 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE M 44 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE M 140 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 282 through 286 Processing sheet with id= AK, first strand: chain 'M' and resid 356 through 361 removed outlier: 6.623A pdb=" N ASN M 382 " --> pdb=" O VAL M 357 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE M 359 " --> pdb=" O ASN M 382 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL M 384 " --> pdb=" O ILE M 359 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ALA M 361 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL M 386 " --> pdb=" O ALA M 361 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR M 387 " --> pdb=" O ILE M 445 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE M 445 " --> pdb=" O THR M 387 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER M 389 " --> pdb=" O ILE M 443 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE M 443 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE M 419 " --> pdb=" O VAL M 412 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL M 412 " --> pdb=" O PHE M 419 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 11.77 Time building geometry restraints manager: 13.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8229 1.33 - 1.45: 7218 1.45 - 1.57: 17270 1.57 - 1.70: 277 1.70 - 1.82: 148 Bond restraints: 33142 Sorted by residual: bond pdb=" C2' AR6 H 501 " pdb=" C3' AR6 H 501 " ideal model delta sigma weight residual 1.532 1.233 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C2' AR6 C 501 " pdb=" C3' AR6 C 501 " ideal model delta sigma weight residual 1.532 1.237 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3D AR6 H 501 " pdb=" C4D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.255 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C3D AR6 C 501 " pdb=" C4D AR6 C 501 " ideal model delta sigma weight residual 1.529 1.258 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C1D AR6 H 501 " pdb=" C2D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.283 0.246 2.00e-02 2.50e+03 1.52e+02 ... (remaining 33137 not shown) Histogram of bond angle deviations from ideal: 94.66 - 102.70: 317 102.70 - 110.74: 11337 110.74 - 118.78: 15704 118.78 - 126.82: 17135 126.82 - 134.86: 883 Bond angle restraints: 45376 Sorted by residual: angle pdb=" CA PRO G 32 " pdb=" N PRO G 32 " pdb=" CD PRO G 32 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.62e+01 angle pdb=" C ALA H 145 " pdb=" CA ALA H 145 " pdb=" CB ALA H 145 " ideal model delta sigma weight residual 116.63 109.91 6.72 1.16e+00 7.43e-01 3.36e+01 angle pdb=" CA PRO G 144 " pdb=" N PRO G 144 " pdb=" CD PRO G 144 " ideal model delta sigma weight residual 112.00 103.90 8.10 1.40e+00 5.10e-01 3.34e+01 angle pdb=" N PRO G 144 " pdb=" CD PRO G 144 " pdb=" CG PRO G 144 " ideal model delta sigma weight residual 103.20 94.66 8.54 1.50e+00 4.44e-01 3.24e+01 angle pdb=" O3A AR6 C 501 " pdb=" PA AR6 C 501 " pdb=" O5' AR6 C 501 " ideal model delta sigma weight residual 93.19 109.95 -16.76 3.00e+00 1.11e-01 3.12e+01 ... (remaining 45371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 19185 33.71 - 67.42: 794 67.42 - 101.12: 44 101.12 - 134.83: 4 134.83 - 168.54: 13 Dihedral angle restraints: 20040 sinusoidal: 9532 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U I 7 " pdb=" C1' U I 7 " pdb=" N1 U I 7 " pdb=" C2 U I 7 " ideal model delta sinusoidal sigma weight residual -160.00 8.54 -168.54 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U O 9 " pdb=" C1' U O 9 " pdb=" N1 U O 9 " pdb=" C2 U O 9 " ideal model delta sinusoidal sigma weight residual 200.00 34.44 165.56 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U N 13 " pdb=" C1' U N 13 " pdb=" N1 U N 13 " pdb=" C2 U N 13 " ideal model delta sinusoidal sigma weight residual 200.00 46.73 153.27 1 1.50e+01 4.44e-03 8.08e+01 ... (remaining 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4785 0.096 - 0.191: 193 0.191 - 0.287: 3 0.287 - 0.383: 2 0.383 - 0.478: 1 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB VAL H 113 " pdb=" CA VAL H 113 " pdb=" CG1 VAL H 113 " pdb=" CG2 VAL H 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C3' AR6 C 501 " pdb=" C2' AR6 C 501 " pdb=" C4' AR6 C 501 " pdb=" O3' AR6 C 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' AR6 H 501 " pdb=" C2' AR6 H 501 " pdb=" C4' AR6 H 501 " pdb=" O3' AR6 H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4981 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 332 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO F 333 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO F 333 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 333 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 31 " 0.094 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO G 32 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 318 " -0.043 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO E 319 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.036 5.00e-02 4.00e+02 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1694 2.72 - 3.27: 32645 3.27 - 3.81: 55087 3.81 - 4.36: 68398 4.36 - 4.90: 111320 Nonbonded interactions: 269144 Sorted by model distance: nonbonded pdb=" O PHE G 373 " pdb=" OG1 THR G 377 " model vdw 2.177 2.440 nonbonded pdb=" OG SER M 493 " pdb=" OD1 ASP M 495 " model vdw 2.180 2.440 nonbonded pdb=" OH TYR F 416 " pdb=" O THR G 404 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR F 221 " pdb=" O TYR F 233 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU M 436 " pdb=" O2' U O 6 " model vdw 2.204 2.440 ... (remaining 269139 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' and resid 1 through 418) selection = chain 'F' selection = (chain 'H' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 7.400 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 88.700 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.270 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 : 0.006 0.299 33142 Z= 0.360 Angle : 0.727 16.758 45376 Z= 0.414 Chirality : 0.042 0.478 4984 Planarity : 0.005 0.146 5238 Dihedral : 17.233 168.539 13248 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.15 % Favored : 94.54 % Rotamer: Outliers : 0.03 % Allowed : 0.06 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.80 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1210 sheet: -0.84 (0.21), residues: 578 loop : -1.27 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 320 HIS 0.005 0.001 HIS G 59 PHE 0.025 0.002 PHE C 343 TYR 0.016 0.001 TYR G 56 ARG 0.005 0.000 ARG F 240 *********************** 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 428 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 3.312 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: B 348 GLU cc_start: 0.7607 (tp30) cc_final: 0.7364 (tp30) REVERT: E 40 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8011 (mtmt) REVERT: E 484 ASP cc_start: 0.7989 (t70) cc_final: 0.7521 (t0) REVERT: F 192 TRP cc_start: 0.6056 (p-90) cc_final: 0.5636 (p-90) REVERT: F 317 LYS cc_start: 0.5364 (mttm) cc_final: 0.5135 (mtmm) REVERT: G 107 ASN cc_start: 0.7008 (t0) cc_final: 0.6595 (t0) REVERT: H 193 MET cc_start: 0.6679 (ttm) cc_final: 0.6425 (mmm) REVERT: H 222 ASP cc_start: 0.5177 (m-30) cc_final: 0.4631 (m-30) REVERT: H 277 MET cc_start: 0.8233 (mmm) cc_final: 0.7955 (mmp) REVERT: M 245 PHE cc_start: 0.7238 (m-10) cc_final: 0.6959 (m-10) REVERT: M 406 LEU cc_start: 0.8975 (mm) cc_final: 0.8767 (mm) outliers start: 1 outliers final: 0 residues processed: 427 average time/residue: 0.4076 time to fit residues: 288.4936 Evaluate side-chains 284 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 3.749 ------------------------------------------------------------------------------- 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: 10.0000 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 0.0050 chunk 282 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 329 HIS E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33142 Z= 0.242 Angle : 0.602 10.441 45376 Z= 0.316 Chirality : 0.043 0.581 4984 Planarity : 0.005 0.103 5238 Dihedral : 17.620 179.679 5960 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.24 % Favored : 94.51 % Rotamer: Outliers : 1.44 % Allowed : 7.98 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.78 (0.14), residues: 3532 helix: 0.79 (0.15), residues: 1208 sheet: -0.93 (0.21), residues: 602 loop : -1.30 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.009 0.001 HIS B 329 PHE 0.033 0.002 PHE A 17 TYR 0.036 0.001 TYR C 190 ARG 0.006 0.000 ARG M 152 *********************** 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 364 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 318 time to evaluate : 3.447 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 287 MET cc_start: 0.5807 (mmm) cc_final: 0.5465 (mmm) REVERT: A 401 VAL cc_start: 0.7355 (t) cc_final: 0.6272 (t) REVERT: B 74 MET cc_start: 0.8269 (ppp) cc_final: 0.8033 (ppp) REVERT: B 348 GLU cc_start: 0.7684 (tp30) cc_final: 0.7467 (tp30) REVERT: E 40 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8541 (mtmt) REVERT: E 106 TYR cc_start: 0.6871 (m-10) cc_final: 0.6638 (m-10) REVERT: E 116 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8065 (t0) REVERT: E 446 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8507 (t160) REVERT: E 484 ASP cc_start: 0.7840 (t70) cc_final: 0.7447 (t0) REVERT: F 190 TYR cc_start: 0.7042 (m-80) cc_final: 0.6389 (m-10) REVERT: F 192 TRP cc_start: 0.5858 (p-90) cc_final: 0.5638 (p-90) REVERT: F 221 TYR cc_start: 0.6339 (m-80) cc_final: 0.5948 (m-80) REVERT: F 277 MET cc_start: 0.7010 (mmt) cc_final: 0.6623 (mmm) REVERT: F 317 LYS cc_start: 0.5407 (mttm) cc_final: 0.5118 (mtmm) REVERT: F 391 PHE cc_start: 0.8670 (p90) cc_final: 0.8419 (p90) REVERT: G 1 MET cc_start: 0.6275 (mmp) cc_final: 0.5508 (mmm) REVERT: G 107 ASN cc_start: 0.6839 (t0) cc_final: 0.6484 (t0) REVERT: G 462 LEU cc_start: 0.7283 (mp) cc_final: 0.7077 (mt) REVERT: H 193 MET cc_start: 0.6514 (ttm) cc_final: 0.6312 (ttm) REVERT: H 308 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.6064 (t) REVERT: H 381 ILE cc_start: 0.7617 (mt) cc_final: 0.7201 (pt) REVERT: M 406 LEU cc_start: 0.9062 (mm) cc_final: 0.8837 (mm) outliers start: 46 outliers final: 32 residues processed: 344 average time/residue: 0.4054 time to fit residues: 236.5508 Evaluate side-chains 308 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 302 LYS Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.0020 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 327 optimal weight: 0.2980 chunk 353 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 GLN M 430 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33142 Z= 0.176 Angle : 0.551 9.048 45376 Z= 0.290 Chirality : 0.041 0.164 4984 Planarity : 0.005 0.081 5238 Dihedral : 17.576 177.548 5960 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.04 % Favored : 94.71 % Rotamer: Outliers : 1.85 % Allowed : 9.79 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.63 (0.14), residues: 3532 helix: 1.01 (0.15), residues: 1184 sheet: -0.84 (0.21), residues: 602 loop : -1.26 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 219 HIS 0.006 0.001 HIS H 320 PHE 0.025 0.001 PHE A 17 TYR 0.012 0.001 TYR G 280 ARG 0.003 0.000 ARG A 263 *********************** 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 370 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 3.788 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 88 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 287 MET cc_start: 0.5762 (mmm) cc_final: 0.5517 (mmm) REVERT: B 74 MET cc_start: 0.8256 (ppp) cc_final: 0.8027 (ppp) REVERT: B 348 GLU cc_start: 0.7692 (tp30) cc_final: 0.7472 (tp30) REVERT: E 40 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8575 (mtmt) REVERT: E 54 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8471 (ptp-110) REVERT: E 81 VAL cc_start: 0.8894 (m) cc_final: 0.8692 (m) REVERT: E 106 TYR cc_start: 0.6862 (m-10) cc_final: 0.6640 (m-10) REVERT: E 484 ASP cc_start: 0.7684 (t70) cc_final: 0.7387 (t0) REVERT: F 190 TYR cc_start: 0.6914 (m-80) cc_final: 0.6490 (m-10) REVERT: F 221 TYR cc_start: 0.6433 (m-80) cc_final: 0.6072 (m-80) REVERT: F 277 MET cc_start: 0.6547 (mmt) cc_final: 0.6241 (mmm) REVERT: F 317 LYS cc_start: 0.5427 (mttm) cc_final: 0.5139 (mtmm) REVERT: F 391 PHE cc_start: 0.8637 (p90) cc_final: 0.8332 (p90) REVERT: G 107 ASN cc_start: 0.6855 (t0) cc_final: 0.6486 (t0) REVERT: G 462 LEU cc_start: 0.7590 (mp) cc_final: 0.7374 (mt) REVERT: H 308 THR cc_start: 0.6512 (OUTLIER) cc_final: 0.6238 (t) REVERT: H 340 HIS cc_start: 0.7225 (m90) cc_final: 0.7021 (m90) REVERT: H 381 ILE cc_start: 0.7688 (mt) cc_final: 0.7241 (pt) REVERT: M 406 LEU cc_start: 0.9045 (mm) cc_final: 0.8800 (mm) outliers start: 59 outliers final: 41 residues processed: 342 average time/residue: 0.4061 time to fit residues: 233.3657 Evaluate side-chains 316 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 273 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.4980 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 328 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 311 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 HIS ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33142 Z= 0.152 Angle : 0.529 8.999 45376 Z= 0.279 Chirality : 0.040 0.171 4984 Planarity : 0.004 0.071 5238 Dihedral : 17.530 175.876 5960 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.93 % Favored : 94.85 % Rotamer: Outliers : 1.63 % Allowed : 11.48 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3532 helix: 1.10 (0.15), residues: 1182 sheet: -0.75 (0.21), residues: 608 loop : -1.23 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 219 HIS 0.006 0.001 HIS G 59 PHE 0.020 0.001 PHE A 17 TYR 0.021 0.001 TYR C 190 ARG 0.005 0.000 ARG H 126 *********************** 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 357 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 305 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 LEU cc_start: 0.8022 (tp) cc_final: 0.7592 (tp) REVERT: A 401 VAL cc_start: 0.6973 (t) cc_final: 0.5234 (t) REVERT: B 74 MET cc_start: 0.8200 (ppp) cc_final: 0.7941 (ppp) REVERT: B 348 GLU cc_start: 0.7666 (tp30) cc_final: 0.7442 (tp30) REVERT: E 40 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8569 (mtmt) REVERT: E 116 ASP cc_start: 0.8223 (m-30) cc_final: 0.7985 (t0) REVERT: E 484 ASP cc_start: 0.7616 (t70) cc_final: 0.7337 (t0) REVERT: F 190 TYR cc_start: 0.7027 (m-80) cc_final: 0.6541 (m-10) REVERT: F 221 TYR cc_start: 0.6433 (m-80) cc_final: 0.6071 (m-80) REVERT: F 277 MET cc_start: 0.6638 (mmt) cc_final: 0.6309 (mmm) REVERT: F 317 LYS cc_start: 0.5398 (mttm) cc_final: 0.5108 (mtmm) REVERT: G 1 MET cc_start: 0.6011 (mmp) cc_final: 0.5717 (mmm) REVERT: G 107 ASN cc_start: 0.6903 (t0) cc_final: 0.6492 (t0) REVERT: G 462 LEU cc_start: 0.7490 (mp) cc_final: 0.7254 (mt) REVERT: H 308 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.6154 (t) REVERT: H 320 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.6070 (m-70) REVERT: H 340 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6730 (m-70) REVERT: H 381 ILE cc_start: 0.7912 (mt) cc_final: 0.7491 (pt) REVERT: M 406 LEU cc_start: 0.9040 (mm) cc_final: 0.8803 (mm) outliers start: 52 outliers final: 36 residues processed: 336 average time/residue: 0.3980 time to fit residues: 229.8722 Evaluate side-chains 311 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 272 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 87 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS C 156 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS E 296 ASN E 446 ASN F 226 HIS ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN M 302 GLN M 329 HIS ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 33142 Z= 0.362 Angle : 0.659 8.612 45376 Z= 0.346 Chirality : 0.044 0.237 4984 Planarity : 0.005 0.069 5238 Dihedral : 17.734 176.825 5960 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.03 % Favored : 93.77 % Rotamer: Outliers : 2.88 % Allowed : 12.27 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3532 helix: 0.90 (0.15), residues: 1176 sheet: -0.96 (0.20), residues: 682 loop : -1.25 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 370 HIS 0.007 0.002 HIS G 59 PHE 0.020 0.002 PHE H 60 TYR 0.028 0.002 TYR B 280 ARG 0.005 0.001 ARG B 295 *********************** 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 376 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 284 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 193 MET cc_start: 0.4870 (ttm) cc_final: 0.4409 (tpt) REVERT: A 401 VAL cc_start: 0.6993 (t) cc_final: 0.6612 (t) REVERT: B 74 MET cc_start: 0.8381 (ppp) cc_final: 0.8091 (ppp) REVERT: B 356 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7078 (tm-30) REVERT: C 103 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6694 (tt) REVERT: E 40 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8485 (mtmt) REVERT: E 484 ASP cc_start: 0.7905 (t70) cc_final: 0.7441 (t0) REVERT: F 190 TYR cc_start: 0.7032 (m-80) cc_final: 0.6584 (m-10) REVERT: F 221 TYR cc_start: 0.6794 (m-80) cc_final: 0.6511 (m-80) REVERT: G 107 ASN cc_start: 0.6895 (t0) cc_final: 0.6567 (t0) REVERT: G 462 LEU cc_start: 0.7755 (mp) cc_final: 0.7525 (mt) REVERT: H 193 MET cc_start: 0.6528 (ttm) cc_final: 0.6191 (ttm) REVERT: H 308 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6257 (t) REVERT: H 381 ILE cc_start: 0.7967 (mt) cc_final: 0.7599 (pt) REVERT: M 406 LEU cc_start: 0.9139 (mm) cc_final: 0.8905 (mm) outliers start: 92 outliers final: 58 residues processed: 339 average time/residue: 0.3894 time to fit residues: 226.6974 Evaluate side-chains 318 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 257 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 200 TYR Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 6.9990 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 0.0470 chunk 182 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN C 226 HIS C 270 ASN C 340 HIS E 296 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33142 Z= 0.253 Angle : 0.580 9.048 45376 Z= 0.305 Chirality : 0.042 0.176 4984 Planarity : 0.005 0.072 5238 Dihedral : 17.687 177.109 5960 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.41 % Favored : 94.39 % Rotamer: Outliers : 2.94 % Allowed : 13.45 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.64 (0.14), residues: 3532 helix: 1.00 (0.15), residues: 1174 sheet: -0.82 (0.20), residues: 658 loop : -1.26 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 370 HIS 0.008 0.001 HIS G 59 PHE 0.018 0.002 PHE G 365 TYR 0.021 0.001 TYR C 190 ARG 0.004 0.000 ARG H 126 *********************** 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 391 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 297 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 74 MET cc_start: 0.8275 (ppp) cc_final: 0.8006 (ppp) REVERT: B 356 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 57 THR cc_start: 0.8286 (m) cc_final: 0.8070 (m) REVERT: C 266 VAL cc_start: 0.9037 (t) cc_final: 0.8837 (m) REVERT: E 104 PHE cc_start: 0.6800 (m-80) cc_final: 0.6545 (t80) REVERT: E 116 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8169 (t70) REVERT: E 285 TYR cc_start: 0.8230 (m-80) cc_final: 0.7764 (m-80) REVERT: E 433 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.4773 (pp) REVERT: E 484 ASP cc_start: 0.7644 (t70) cc_final: 0.7260 (t0) REVERT: F 190 TYR cc_start: 0.7035 (m-80) cc_final: 0.6767 (m-80) REVERT: F 193 MET cc_start: 0.3353 (mmt) cc_final: 0.2819 (tpp) REVERT: F 221 TYR cc_start: 0.6750 (m-80) cc_final: 0.6488 (m-80) REVERT: F 229 LYS cc_start: 0.5754 (ttmt) cc_final: 0.5045 (mmmt) REVERT: F 309 MET cc_start: 0.7020 (tmm) cc_final: 0.6803 (tmm) REVERT: G 1 MET cc_start: 0.5501 (mmp) cc_final: 0.5055 (mmm) REVERT: G 107 ASN cc_start: 0.6901 (t0) cc_final: 0.6565 (t0) REVERT: G 148 TYR cc_start: 0.8002 (t80) cc_final: 0.7061 (t80) REVERT: G 462 LEU cc_start: 0.7749 (mp) cc_final: 0.7443 (mt) REVERT: H 193 MET cc_start: 0.6640 (ttm) cc_final: 0.6283 (ttm) REVERT: H 308 THR cc_start: 0.6309 (OUTLIER) cc_final: 0.6021 (t) REVERT: H 340 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.7341 (m90) REVERT: H 381 ILE cc_start: 0.8034 (mt) cc_final: 0.7632 (pt) REVERT: M 150 TYR cc_start: 0.8040 (m-10) cc_final: 0.7811 (m-80) outliers start: 94 outliers final: 60 residues processed: 358 average time/residue: 0.4557 time to fit residues: 281.6517 Evaluate side-chains 335 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 270 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 245 GLU Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 340 HIS Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 340 HIS E 296 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 357 GLN ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33142 Z= 0.272 Angle : 0.600 10.609 45376 Z= 0.313 Chirality : 0.042 0.177 4984 Planarity : 0.005 0.071 5238 Dihedral : 17.662 177.335 5960 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.97 % Favored : 93.83 % Rotamer: Outliers : 2.97 % Allowed : 14.27 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.68 (0.14), residues: 3532 helix: 0.98 (0.15), residues: 1176 sheet: -0.95 (0.20), residues: 654 loop : -1.24 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 421 HIS 0.007 0.001 HIS C 188 PHE 0.020 0.002 PHE E 104 TYR 0.018 0.001 TYR B 280 ARG 0.011 0.000 ARG H 263 *********************** 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 379 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 284 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 287 MET cc_start: 0.5842 (mmm) cc_final: 0.5464 (tpp) REVERT: B 74 MET cc_start: 0.8264 (ppp) cc_final: 0.7994 (ppp) REVERT: B 356 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 57 THR cc_start: 0.8318 (m) cc_final: 0.8080 (m) REVERT: C 266 VAL cc_start: 0.9079 (t) cc_final: 0.8849 (m) REVERT: E 106 TYR cc_start: 0.6283 (m-10) cc_final: 0.5838 (m-10) REVERT: E 285 TYR cc_start: 0.8212 (m-80) cc_final: 0.7745 (m-80) REVERT: E 484 ASP cc_start: 0.7671 (t70) cc_final: 0.7268 (t0) REVERT: F 40 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6866 (p0) REVERT: F 190 TYR cc_start: 0.6922 (m-80) cc_final: 0.6624 (m-10) REVERT: F 193 MET cc_start: 0.3332 (mmt) cc_final: 0.2624 (tpp) REVERT: F 221 TYR cc_start: 0.6800 (m-80) cc_final: 0.6570 (m-80) REVERT: F 229 LYS cc_start: 0.5802 (ttmt) cc_final: 0.5150 (mmmt) REVERT: G 1 MET cc_start: 0.5532 (mmp) cc_final: 0.5007 (mmm) REVERT: G 107 ASN cc_start: 0.6923 (t0) cc_final: 0.6611 (t0) REVERT: G 148 TYR cc_start: 0.7989 (t80) cc_final: 0.7063 (t80) REVERT: G 462 LEU cc_start: 0.7742 (mp) cc_final: 0.7452 (mt) REVERT: H 193 MET cc_start: 0.6800 (ttm) cc_final: 0.6445 (ttm) REVERT: H 308 THR cc_start: 0.6352 (OUTLIER) cc_final: 0.6047 (t) REVERT: H 381 ILE cc_start: 0.8116 (mt) cc_final: 0.7721 (pt) outliers start: 95 outliers final: 68 residues processed: 347 average time/residue: 0.3885 time to fit residues: 230.6292 Evaluate side-chains 333 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 245 GLU Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 161 MET Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR 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: 2.9990 chunk 207 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS E 296 ASN E 446 ASN F 138 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 GLN ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33142 Z= 0.182 Angle : 0.551 9.182 45376 Z= 0.287 Chirality : 0.041 0.180 4984 Planarity : 0.004 0.068 5238 Dihedral : 17.562 175.098 5960 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.10 % Favored : 94.71 % Rotamer: Outliers : 2.60 % Allowed : 15.36 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3532 helix: 1.13 (0.15), residues: 1172 sheet: -0.86 (0.21), residues: 644 loop : -1.17 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 421 HIS 0.008 0.001 HIS A 320 PHE 0.018 0.001 PHE G 224 TYR 0.016 0.001 TYR H 330 ARG 0.009 0.000 ARG H 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 367 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 284 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7964 (mm) REVERT: A 193 MET cc_start: 0.4885 (ttm) cc_final: 0.4662 (tpt) REVERT: B 356 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 57 THR cc_start: 0.8274 (m) cc_final: 0.8062 (m) REVERT: C 266 VAL cc_start: 0.9018 (t) cc_final: 0.8747 (m) REVERT: E 106 TYR cc_start: 0.6026 (m-10) cc_final: 0.5757 (m-10) REVERT: E 116 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8160 (t70) REVERT: E 364 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7510 (mtt90) REVERT: E 446 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8456 (t160) REVERT: E 484 ASP cc_start: 0.7602 (t70) cc_final: 0.7217 (t0) REVERT: F 190 TYR cc_start: 0.6887 (m-80) cc_final: 0.6583 (m-10) REVERT: F 193 MET cc_start: 0.3566 (mmt) cc_final: 0.3112 (tpp) REVERT: F 221 TYR cc_start: 0.6715 (m-80) cc_final: 0.6484 (m-80) REVERT: F 229 LYS cc_start: 0.5737 (ttmt) cc_final: 0.5074 (mmmt) REVERT: G 1 MET cc_start: 0.5455 (mmp) cc_final: 0.4902 (mmm) REVERT: G 107 ASN cc_start: 0.6916 (t0) cc_final: 0.6591 (t0) REVERT: G 148 TYR cc_start: 0.7930 (t80) cc_final: 0.6946 (t80) REVERT: G 462 LEU cc_start: 0.7859 (mp) cc_final: 0.7563 (mt) REVERT: H 193 MET cc_start: 0.6758 (ttm) cc_final: 0.6434 (ttm) REVERT: H 254 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7072 (m-40) REVERT: H 308 THR cc_start: 0.6384 (OUTLIER) cc_final: 0.6103 (t) REVERT: H 381 ILE cc_start: 0.8127 (mt) cc_final: 0.7736 (pt) outliers start: 83 outliers final: 56 residues processed: 341 average time/residue: 0.3828 time to fit residues: 223.2619 Evaluate side-chains 328 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 266 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 234 HIS Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 437 VAL Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.0030 chunk 332 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 446 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33142 Z= 0.344 Angle : 0.645 12.664 45376 Z= 0.335 Chirality : 0.043 0.227 4984 Planarity : 0.005 0.070 5238 Dihedral : 17.639 176.436 5960 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.48 % Favored : 93.37 % Rotamer: Outliers : 2.50 % Allowed : 15.93 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.75 (0.14), residues: 3532 helix: 0.91 (0.15), residues: 1178 sheet: -1.02 (0.20), residues: 668 loop : -1.26 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 421 HIS 0.008 0.002 HIS A 320 PHE 0.019 0.002 PHE H 342 TYR 0.025 0.002 TYR M 150 ARG 0.008 0.001 ARG H 263 *********************** 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 344 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 264 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 193 MET cc_start: 0.5005 (ttm) cc_final: 0.4571 (tpp) REVERT: A 320 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7286 (m170) REVERT: B 356 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 57 THR cc_start: 0.8324 (m) cc_final: 0.8076 (m) REVERT: E 106 TYR cc_start: 0.5988 (m-10) cc_final: 0.5603 (m-10) REVERT: E 484 ASP cc_start: 0.7696 (t70) cc_final: 0.7300 (t0) REVERT: F 190 TYR cc_start: 0.6953 (m-80) cc_final: 0.6665 (m-10) REVERT: F 193 MET cc_start: 0.2971 (mmt) cc_final: 0.2573 (mmt) REVERT: F 221 TYR cc_start: 0.6825 (m-80) cc_final: 0.6618 (m-80) REVERT: F 229 LYS cc_start: 0.5850 (ttmt) cc_final: 0.5340 (mmmt) REVERT: G 1 MET cc_start: 0.5547 (mmp) cc_final: 0.5077 (mmm) REVERT: G 107 ASN cc_start: 0.6956 (t0) cc_final: 0.6607 (t0) REVERT: G 148 TYR cc_start: 0.8015 (t80) cc_final: 0.7073 (t80) REVERT: G 462 LEU cc_start: 0.7760 (mp) cc_final: 0.7522 (mt) REVERT: H 193 MET cc_start: 0.6769 (ttm) cc_final: 0.6378 (ttm) REVERT: H 308 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.6169 (t) REVERT: H 381 ILE cc_start: 0.8189 (mt) cc_final: 0.7803 (pt) outliers start: 80 outliers final: 59 residues processed: 319 average time/residue: 0.3969 time to fit residues: 217.2925 Evaluate side-chains 319 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 257 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 405 ILE Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 245 GLU Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 234 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 340 HIS E 296 ASN E 446 ASN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 ASN ** M 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33142 Z= 0.210 Angle : 0.578 9.849 45376 Z= 0.299 Chirality : 0.041 0.224 4984 Planarity : 0.004 0.068 5238 Dihedral : 17.563 173.919 5960 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.21 % Favored : 94.65 % Rotamer: Outliers : 2.10 % Allowed : 16.58 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -0.59 (0.14), residues: 3532 helix: 1.08 (0.15), residues: 1174 sheet: -0.93 (0.21), residues: 628 loop : -1.20 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP M 421 HIS 0.008 0.001 HIS A 320 PHE 0.020 0.001 PHE H 332 TYR 0.019 0.001 TYR B 56 ARG 0.008 0.000 ARG H 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 341 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 274 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 193 MET cc_start: 0.5308 (ttm) cc_final: 0.4823 (tpp) REVERT: B 356 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7161 (tm-30) REVERT: B 403 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.3963 (m-10) REVERT: B 416 ARG cc_start: 0.7436 (mmt180) cc_final: 0.7228 (mpt180) REVERT: C 57 THR cc_start: 0.8334 (m) cc_final: 0.8101 (m) REVERT: C 266 VAL cc_start: 0.9046 (t) cc_final: 0.8806 (m) REVERT: E 106 TYR cc_start: 0.5963 (m-10) cc_final: 0.5569 (m-10) REVERT: E 484 ASP cc_start: 0.7663 (t70) cc_final: 0.7262 (t0) REVERT: F 190 TYR cc_start: 0.6877 (m-80) cc_final: 0.6592 (m-10) REVERT: F 193 MET cc_start: 0.3495 (mmt) cc_final: 0.3181 (mmt) REVERT: F 221 TYR cc_start: 0.6622 (m-80) cc_final: 0.6416 (m-80) REVERT: F 229 LYS cc_start: 0.6162 (ttmt) cc_final: 0.5657 (mmmt) REVERT: G 1 MET cc_start: 0.5486 (mmp) cc_final: 0.4899 (mmm) REVERT: G 107 ASN cc_start: 0.7001 (t0) cc_final: 0.6625 (t0) REVERT: G 148 TYR cc_start: 0.7977 (t80) cc_final: 0.6966 (t80) REVERT: G 462 LEU cc_start: 0.7696 (mp) cc_final: 0.7420 (mt) REVERT: H 193 MET cc_start: 0.6772 (ttm) cc_final: 0.6398 (ttm) REVERT: H 254 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: H 308 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6244 (t) REVERT: H 381 ILE cc_start: 0.8169 (mt) cc_final: 0.7785 (pt) outliers start: 67 outliers final: 56 residues processed: 320 average time/residue: 0.4165 time to fit residues: 228.9918 Evaluate side-chains 319 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 259 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 470 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 6 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 426 VAL Chi-restraints excluded: chain G residue 434 SER Chi-restraints excluded: chain G residue 498 THR Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 234 HIS Chi-restraints excluded: chain H residue 254 ASN Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 494 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 263 optimal weight: 0.0870 chunk 42 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 0.0050 chunk 119 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 267 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS E 296 ASN E 446 ASN F 138 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 ASN ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 360 HIS ** M 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094020 restraints weight = 87374.902| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.24 r_work: 0.3513 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33142 Z= 0.154 Angle : 0.554 8.432 45376 Z= 0.284 Chirality : 0.041 0.460 4984 Planarity : 0.004 0.067 5238 Dihedral : 17.400 170.291 5960 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.68 % Rotamer: Outliers : 1.66 % Allowed : 17.37 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.46 (0.14), residues: 3532 helix: 1.15 (0.15), residues: 1186 sheet: -0.74 (0.21), residues: 618 loop : -1.16 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 421 HIS 0.007 0.001 HIS G 59 PHE 0.019 0.001 PHE E 104 TYR 0.013 0.001 TYR B 56 ARG 0.012 0.000 ARG H 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6242.45 seconds wall clock time: 116 minutes 18.56 seconds (6978.56 seconds total)