Starting phenix.real_space_refine on Tue Nov 21 08:49:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oz6_17299/11_2023/8oz6_17299.pdb" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 132 5.49 5 S 96 5.16 5 C 20236 2.51 5 N 5300 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 387": "OD1" <-> "OD2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 40": "OD1" <-> "OD2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G GLU 306": "OE1" <-> "OE2" Residue "G GLU 394": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 133": "OD1" <-> "OD2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 444": "OE1" <-> "OE2" Residue "H GLU 449": "OE1" <-> "OE2" Residue "H GLU 488": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 32004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 16.04, per 1000 atoms: 0.50 Number of scatterers: 32004 At special positions: 0 Unit cell: (177.87, 208.12, 165.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 132 15.00 O 6240 8.00 N 5300 7.00 C 20236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.66 Conformation dependent library (CDL) restraints added in 5.7 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 28 sheets defined 39.3% alpha, 14.3% beta 11 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 10.54 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.825A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.081A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.037A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.118A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.522A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.682A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.865A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.695A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.537A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.672A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.716A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.824A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.529A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.526A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.928A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.558A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.168A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.300A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.541A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.537A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 353 through 366 removed outlier: 3.557A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.797A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 46 through 62 removed outlier: 4.095A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.642A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.702A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.568A pdb=" N VAL D 162 " --> pdb=" O LYS D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.523A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.841A pdb=" N ALA D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.852A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.710A pdb=" N ASP D 458 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.789A pdb=" N ASP D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.718A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.626A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.838A pdb=" N PHE E 93 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 94' Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.528A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 157 removed outlier: 3.654A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.056A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.548A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.950A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 4.527A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.086A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.778A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 132 removed outlier: 4.173A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 3.549A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.692A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 218 Processing helix chain 'F' and resid 230 through 234 removed outlier: 3.750A pdb=" N ASP F 233 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.505A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.518A pdb=" N TYR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.596A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.837A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.550A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'G' and resid 10 through 13 removed outlier: 3.801A pdb=" N ASP G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.939A pdb=" N THR G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 65 through 70 removed outlier: 4.612A pdb=" N GLN G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.729A pdb=" N ILE G 108 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.913A pdb=" N GLY G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 removed outlier: 3.678A pdb=" N PHE G 158 " --> pdb=" O TYR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.684A pdb=" N ASP G 222 " --> pdb=" O TRP G 219 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR G 224 " --> pdb=" O TYR G 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 224' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.575A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 242 through 249 removed outlier: 3.519A pdb=" N ILE G 246 " --> pdb=" O PRO G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 280 removed outlier: 4.233A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 353 through 367 removed outlier: 4.180A pdb=" N ASN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.905A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.637A pdb=" N GLY H 17 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 31 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.737A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 97 through 106 Processing helix chain 'H' and resid 109 through 132 removed outlier: 4.028A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.170A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.679A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.590A pdb=" N ALA H 259 " --> pdb=" O THR H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 348 removed outlier: 3.660A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.550A pdb=" N TRP H 370 " --> pdb=" O ASN H 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.578A pdb=" N ASP H 458 " --> pdb=" O GLN H 454 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.630A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.788A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.902A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 62 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 415 removed outlier: 8.367A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3 through 6 current: chain 'B' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 316 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.583A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.513A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.671A pdb=" N THR B 92 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 305 removed outlier: 3.655A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.584A pdb=" N LYS C 4 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 172 removed outlier: 8.431A pdb=" N LEU D 4 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 411 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR D 6 " --> pdb=" O LYS C 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 6 current: chain 'D' and resid 298 through 305 removed outlier: 3.539A pdb=" N PHE D 304 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 312 " --> pdb=" O PHE D 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 315 current: chain 'D' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 389 current: chain 'D' and resid 417 through 420 Processing sheet with id=AB1, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.297A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 334 " --> pdb=" O LYS C 328 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.588A pdb=" N THR D 92 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 425 through 426 removed outlier: 3.803A pdb=" N VAL D 426 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 5.831A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 4 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 291 through 294 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 removed outlier: 8.672A pdb=" N LEU F 4 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 3 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 3.534A pdb=" N PHE F 304 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F 312 " --> pdb=" O PHE F 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 315 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AB9, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.589A pdb=" N GLN F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.328A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.921A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 32 through 33 removed outlier: 5.622A pdb=" N ILE G 5 " --> pdb=" O TRP G 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS G 4 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU G 61 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE G 6 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 63 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 8 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 165 through 178 current: chain 'G' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 291 through 294 current: chain 'G' and resid 317 through 328 removed outlier: 3.639A pdb=" N VAL G 334 " --> pdb=" O LYS G 328 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 415 removed outlier: 4.302A pdb=" N ASN G 413 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR H 6 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N SER G 415 " --> pdb=" O TYR H 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 3.527A pdb=" N PHE H 304 " --> pdb=" O VAL H 312 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 316 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 188 Processing sheet with id=AC8, first strand: chain 'G' and resid 304 through 305 Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 92 through 95 removed outlier: 7.099A pdb=" N SER H 41 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS H 94 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 43 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 999 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 11.94 Time building geometry restraints manager: 14.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3965 1.24 - 1.38: 8709 1.38 - 1.53: 15872 1.53 - 1.67: 4370 1.67 - 1.81: 148 Bond restraints: 33064 Sorted by residual: bond pdb=" CG PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.503 1.098 0.405 3.40e-02 8.65e+02 1.42e+02 bond pdb=" CG PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO F 158 " pdb=" CD PRO F 158 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+02 bond pdb=" CG PRO D 500 " pdb=" CD PRO D 500 " ideal model delta sigma weight residual 1.503 1.305 0.198 3.40e-02 8.65e+02 3.40e+01 bond pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.14e+01 ... (remaining 33059 not shown) Histogram of bond angle deviations from ideal: 81.54 - 93.14: 7 93.14 - 104.75: 973 104.75 - 116.35: 21948 116.35 - 127.95: 21920 127.95 - 139.55: 408 Bond angle restraints: 45256 Sorted by residual: angle pdb=" N PRO D 378 " pdb=" CD PRO D 378 " pdb=" CG PRO D 378 " ideal model delta sigma weight residual 103.20 81.54 21.66 1.50e+00 4.44e-01 2.08e+02 angle pdb=" N PRO D 76 " pdb=" CD PRO D 76 " pdb=" CG PRO D 76 " ideal model delta sigma weight residual 103.20 82.69 20.51 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO F 158 " pdb=" CD PRO F 158 " pdb=" CG PRO F 158 " ideal model delta sigma weight residual 103.20 83.55 19.65 1.50e+00 4.44e-01 1.72e+02 angle pdb=" CA PRO D 378 " pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 112.00 98.26 13.74 1.40e+00 5.10e-01 9.64e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 ... (remaining 45251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 18889 35.69 - 71.37: 467 71.37 - 107.06: 33 107.06 - 142.74: 8 142.74 - 178.43: 7 Dihedral angle restraints: 19404 sinusoidal: 8896 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 21.57 178.43 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 9 " pdb=" C1' U M 9 " pdb=" N1 U M 9 " pdb=" C2 U M 9 " ideal model delta sinusoidal sigma weight residual -160.00 -7.26 -152.74 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 48.79 151.21 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 19401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3585 0.038 - 0.076: 1001 0.076 - 0.114: 312 0.114 - 0.152: 64 0.152 - 0.190: 6 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA PRO D 427 " pdb=" N PRO D 427 " pdb=" C PRO D 427 " pdb=" CB PRO D 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TYR D 56 " pdb=" N TYR D 56 " pdb=" C TYR D 56 " pdb=" CB TYR D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4965 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 499 " -0.065 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 500 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 254 " -0.019 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" CG TRP D 254 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP D 254 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 254 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 157 " -0.063 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 158 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " -0.048 5.00e-02 4.00e+02 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 631 2.65 - 3.22: 30314 3.22 - 3.78: 52738 3.78 - 4.34: 73379 4.34 - 4.90: 112902 Nonbonded interactions: 269964 Sorted by model distance: nonbonded pdb=" OG SER C 354 " pdb=" O2' U K 8 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR A 416 " pdb=" O THR B 404 " model vdw 2.122 2.440 nonbonded pdb=" OD1 ASN A 151 " pdb=" NE2 GLN A 155 " model vdw 2.131 2.520 nonbonded pdb=" OH TYR C 190 " pdb=" O ALA C 220 " model vdw 2.134 2.440 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.140 2.440 ... (remaining 269959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 7.570 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 90.120 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.250 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.405 33064 Z= 0.312 Angle : 0.734 21.656 45256 Z= 0.433 Chirality : 0.040 0.190 4968 Planarity : 0.005 0.091 5236 Dihedral : 15.690 178.426 12612 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.95 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.11 (0.15), residues: 1190 sheet: -1.09 (0.21), residues: 612 loop : -1.13 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.4519 time to fit residues: 305.3182 Evaluate side-chains 271 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.979 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 0.0070 chunk 184 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 282 optimal weight: 0.0050 chunk 109 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 3.9990 overall best weight: 0.5412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS E 116 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS F 439 ASN F 466 ASN G 109 ASN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33064 Z= 0.184 Angle : 0.620 10.224 45256 Z= 0.324 Chirality : 0.042 0.194 4968 Planarity : 0.005 0.057 5236 Dihedral : 15.077 160.722 5324 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.84 % Favored : 94.85 % Rotamer: Outliers : 1.22 % Allowed : 8.79 % Favored : 89.99 % 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: -0.95 (0.14), residues: 3532 helix: 0.32 (0.15), residues: 1206 sheet: -1.04 (0.21), residues: 626 loop : -1.10 (0.15), residues: 1700 *********************** 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 372 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 333 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 347 average time/residue: 0.4653 time to fit residues: 263.7521 Evaluate side-chains 283 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3514 time to fit residues: 19.8296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 293 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 ASN G 102 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN H 329 HIS ** H 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 33064 Z= 0.429 Angle : 0.839 10.189 45256 Z= 0.443 Chirality : 0.047 0.193 4968 Planarity : 0.006 0.087 5236 Dihedral : 15.717 161.329 5324 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 2.47 % Allowed : 12.45 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3532 helix: -0.30 (0.14), residues: 1214 sheet: -1.45 (0.21), residues: 566 loop : -1.32 (0.14), residues: 1752 *********************** 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 356 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 277 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 47 residues processed: 338 average time/residue: 0.4335 time to fit residues: 242.6723 Evaluate side-chains 294 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 247 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3282 time to fit residues: 32.3667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 347 optimal weight: 10.0000 chunk 171 optimal weight: 0.0870 chunk 311 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 209 GLN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33064 Z= 0.183 Angle : 0.622 10.814 45256 Z= 0.322 Chirality : 0.042 0.227 4968 Planarity : 0.004 0.058 5236 Dihedral : 15.537 162.882 5324 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.04 % Favored : 94.65 % Rotamer: Outliers : 1.22 % Allowed : 14.24 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3532 helix: 0.35 (0.15), residues: 1216 sheet: -1.38 (0.21), residues: 576 loop : -1.14 (0.15), residues: 1740 *********************** 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 331 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 292 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 315 average time/residue: 0.4713 time to fit residues: 245.4684 Evaluate side-chains 274 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 3.926 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3214 time to fit residues: 16.1765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 296 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.0000 chunk 312 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 318 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 33064 Z= 0.261 Angle : 0.669 15.525 45256 Z= 0.347 Chirality : 0.043 0.195 4968 Planarity : 0.005 0.062 5236 Dihedral : 15.570 163.399 5324 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 1.60 % Allowed : 16.18 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3532 helix: 0.34 (0.15), residues: 1228 sheet: -1.48 (0.21), residues: 570 loop : -1.20 (0.15), residues: 1734 *********************** 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 325 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 274 time to evaluate : 3.951 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 outliers start: 51 outliers final: 26 residues processed: 305 average time/residue: 0.4188 time to fit residues: 213.4269 Evaluate side-chains 277 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3196 time to fit residues: 19.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33064 Z= 0.199 Angle : 0.632 11.968 45256 Z= 0.325 Chirality : 0.042 0.185 4968 Planarity : 0.005 0.061 5236 Dihedral : 15.546 165.082 5324 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.58 % Favored : 94.11 % Rotamer: Outliers : 1.50 % Allowed : 17.02 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3532 helix: 0.53 (0.15), residues: 1218 sheet: -1.37 (0.22), residues: 556 loop : -1.17 (0.15), residues: 1758 *********************** 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 323 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 3.643 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 outliers start: 48 outliers final: 16 residues processed: 306 average time/residue: 0.4292 time to fit residues: 218.3516 Evaluate side-chains 266 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 250 time to evaluate : 3.589 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3015 time to fit residues: 13.6706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 129 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33064 Z= 0.294 Angle : 0.706 12.803 45256 Z= 0.369 Chirality : 0.044 0.213 4968 Planarity : 0.005 0.067 5236 Dihedral : 15.672 164.970 5324 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.05 % Favored : 92.67 % Rotamer: Outliers : 2.03 % Allowed : 17.15 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3532 helix: 0.23 (0.15), residues: 1234 sheet: -1.65 (0.21), residues: 558 loop : -1.34 (0.15), residues: 1740 *********************** 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 325 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 260 time to evaluate : 3.976 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 outliers start: 65 outliers final: 39 residues processed: 304 average time/residue: 0.4370 time to fit residues: 219.8078 Evaluate side-chains 283 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 3.551 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3042 time to fit residues: 26.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS F 135 ASN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33064 Z= 0.180 Angle : 0.643 13.167 45256 Z= 0.328 Chirality : 0.042 0.228 4968 Planarity : 0.004 0.061 5236 Dihedral : 15.581 167.123 5324 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.42 % Rotamer: Outliers : 0.75 % Allowed : 18.12 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3532 helix: 0.61 (0.15), residues: 1206 sheet: -1.41 (0.21), residues: 558 loop : -1.23 (0.15), residues: 1768 *********************** 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 310 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 3.581 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 outliers start: 24 outliers final: 9 residues processed: 304 average time/residue: 0.4406 time to fit residues: 219.7055 Evaluate side-chains 265 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 3.568 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3231 time to fit residues: 10.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 303 optimal weight: 20.0000 chunk 323 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33064 Z= 0.246 Angle : 0.680 13.179 45256 Z= 0.350 Chirality : 0.043 0.253 4968 Planarity : 0.005 0.062 5236 Dihedral : 15.612 166.809 5324 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 0.75 % Allowed : 19.24 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3532 helix: 0.50 (0.15), residues: 1218 sheet: -1.52 (0.22), residues: 530 loop : -1.31 (0.15), residues: 1784 *********************** 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 271 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 3.718 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 outliers start: 24 outliers final: 18 residues processed: 262 average time/residue: 0.4389 time to fit residues: 190.8282 Evaluate side-chains 259 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 3.674 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2979 time to fit residues: 14.9374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 208 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 237 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 0.6980 chunk 285 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 314 GLN B 207 HIS E 340 HIS ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33064 Z= 0.184 Angle : 0.653 13.758 45256 Z= 0.331 Chirality : 0.042 0.237 4968 Planarity : 0.004 0.061 5236 Dihedral : 15.591 169.435 5324 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 0.25 % Allowed : 19.49 % Favored : 80.26 % 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: -0.92 (0.14), residues: 3532 helix: 0.64 (0.15), residues: 1210 sheet: -1.35 (0.22), residues: 526 loop : -1.23 (0.15), residues: 1796 ********************** 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 278 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 3.795 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 outliers start: 8 outliers final: 7 residues processed: 275 average time/residue: 0.4628 time to fit residues: 209.0957 Evaluate side-chains 259 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 252 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3383 time to fit residues: 9.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 286 optimal weight: 20.0000 chunk 119 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 129 ASN D 322 ASN E 340 HIS ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 382 ASN ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.105071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.089306 restraints weight = 204177.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.090693 restraints weight = 146198.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.091611 restraints weight = 115814.100| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33064 Z= 0.220 Angle : 0.675 16.036 45256 Z= 0.341 Chirality : 0.043 0.224 4968 Planarity : 0.005 0.065 5236 Dihedral : 15.616 169.720 5324 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.16 % Favored : 92.64 % Rotamer: Outliers : 0.44 % Allowed : 19.81 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3532 helix: 0.59 (0.15), residues: 1210 sheet: -1.46 (0.22), residues: 540 loop : -1.26 (0.15), residues: 1782 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5960.78 seconds wall clock time: 112 minutes 1.56 seconds (6721.56 seconds total)