Starting phenix.real_space_refine on Tue Apr 9 22:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jt6_36634/04_2024/8jt6_36634_neut_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 5674 2.51 5 N 1465 2.21 5 O 1624 1.98 5 F 1 1.80 5 H 8554 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R ARG 65": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 227": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 339": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 341": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17383 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3537 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 4945 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "E" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3471 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 698 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4497 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 235 Unusual residues: {'CLR': 5, 'EZX': 1, 'J40': 1, 'PLM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'J40:plan-1': 1, 'J40:plan-3': 1, 'J40:plan-4': 1, 'J40:plan-5': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 8.46, per 1000 atoms: 0.49 Number of scatterers: 17383 At special positions: 0 Unit cell: (111.72, 136.08, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 63 16.00 P 2 15.00 F 1 9.00 O 1624 8.00 N 1465 7.00 C 5674 6.00 H 8554 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.62 Conformation dependent library (CDL) restraints added in 2.0 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 removed outlier: 3.601A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.554A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.670A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.973A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.793A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 36 through 63 Processing helix chain 'R' and resid 70 through 88 Processing helix chain 'R' and resid 90 through 99 Processing helix chain 'R' and resid 106 through 139 removed outlier: 3.679A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 146 Processing helix chain 'R' and resid 150 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 227 Processing helix chain 'R' and resid 325 through 371 removed outlier: 3.563A pdb=" N GLY R 352 " --> pdb=" O ILE R 349 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU R 359 " --> pdb=" O LEU R 356 " (cutoff:3.500A) Proline residue: R 360 - end of helix removed outlier: 4.172A pdb=" N LEU R 368 " --> pdb=" O ALA R 365 " (cutoff:3.500A) Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 379 through 401 removed outlier: 3.634A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.731A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.909A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.441A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.583A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 263 through 265 removed outlier: 4.685A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.224A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.598A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.504A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.678A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 390 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.36 Time building geometry restraints manager: 14.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8520 1.03 - 1.23: 42 1.23 - 1.42: 3738 1.42 - 1.62: 5170 1.62 - 1.81: 107 Bond restraints: 17577 Sorted by residual: bond pdb=" C17 EZX R 509 " pdb=" C7 EZX R 509 " ideal model delta sigma weight residual 1.416 1.117 0.299 2.00e-02 2.50e+03 2.24e+02 bond pdb=" C11 CLR R 502 " pdb=" C9 CLR R 502 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 504 " pdb=" C9 CLR R 504 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 501 " pdb=" C9 CLR R 501 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 506 " pdb=" C9 CLR R 506 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 17572 not shown) Histogram of bond angle deviations from ideal: 95.44 - 104.22: 119 104.22 - 112.99: 20335 112.99 - 121.77: 7912 121.77 - 130.55: 3161 130.55 - 139.33: 43 Bond angle restraints: 31570 Sorted by residual: angle pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" CD PRO E 75 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" C6 EZX R 509 " pdb=" N2 EZX R 509 " pdb=" C7 EZX R 509 " ideal model delta sigma weight residual 87.71 108.32 -20.61 3.00e+00 1.11e-01 4.72e+01 angle pdb=" C10 EZX R 509 " pdb=" C11 EZX R 509 " pdb=" N3 EZX R 509 " ideal model delta sigma weight residual 119.95 137.82 -17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" CA PRO R 369 " pdb=" N PRO R 369 " pdb=" CD PRO R 369 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" C12 EZX R 509 " pdb=" C13 EZX R 509 " pdb=" C14 EZX R 509 " ideal model delta sigma weight residual 123.51 139.33 -15.82 3.00e+00 1.11e-01 2.78e+01 ... (remaining 31565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 8180 27.39 - 54.79: 312 54.79 - 82.18: 49 82.18 - 109.57: 6 109.57 - 136.97: 3 Dihedral angle restraints: 8550 sinusoidal: 4754 harmonic: 3796 Sorted by residual: dihedral pdb=" C6 EZX R 509 " pdb=" C7 EZX R 509 " pdb=" N2 EZX R 509 " pdb=" C8 EZX R 509 " ideal model delta sinusoidal sigma weight residual -121.36 15.61 -136.97 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" N ILE B 273 " pdb=" CA ILE B 273 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C15 EZX R 509 " pdb=" C16 EZX R 509 " pdb=" N1 EZX R 509 " pdb=" C5 EZX R 509 " ideal model delta sinusoidal sigma weight residual -52.92 64.49 -117.41 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 8547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.040: 1397 1.040 - 2.081: 0 2.081 - 3.121: 0 3.121 - 4.161: 0 4.161 - 5.202: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C4 J40 R 508 " pdb=" C3 J40 R 508 " pdb=" C5 J40 R 508 " pdb=" O4 J40 R 508 " both_signs ideal model delta sigma weight residual False -2.50 2.70 -5.20 2.00e-01 2.50e+01 6.76e+02 chirality pdb=" C1 J40 R 508 " pdb=" C2 J40 R 508 " pdb=" C6 J40 R 508 " pdb=" O1 J40 R 508 " both_signs ideal model delta sigma weight residual False -2.51 2.00 -4.51 2.00e-01 2.50e+01 5.09e+02 chirality pdb=" C9 CLR R 502 " pdb=" C10 CLR R 502 " pdb=" C11 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.45 -2.83 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1396 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 J40 R 508 " 0.084 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C31 J40 R 508 " -0.024 2.00e-02 2.50e+03 pdb=" O18 J40 R 508 " -0.027 2.00e-02 2.50e+03 pdb=" O19 J40 R 508 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.087 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO E 75 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 368 " 0.070 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 369 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 369 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 369 " 0.055 5.00e-02 4.00e+02 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 728 2.18 - 2.79: 34048 2.79 - 3.39: 46613 3.39 - 4.00: 60866 4.00 - 4.60: 95048 Nonbonded interactions: 237303 Sorted by model distance: nonbonded pdb=" HG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP B 195 " pdb=" H ARG B 197 " model vdw 1.583 1.850 nonbonded pdb="HH12 ARG B 22 " pdb=" O ASP B 258 " model vdw 1.590 1.850 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.621 1.850 nonbonded pdb=" OD1 ASN A 269 " pdb=" HG1 THR A 324 " model vdw 1.641 1.850 ... (remaining 237298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 6.980 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 57.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.012 0.299 9023 Z= 0.822 Angle : 0.772 20.615 12243 Z= 0.366 Chirality : 0.191 5.202 1399 Planarity : 0.005 0.121 1502 Dihedral : 14.093 136.967 3526 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.27), residues: 1080 helix: 3.56 (0.28), residues: 360 sheet: 1.48 (0.32), residues: 271 loop : 0.37 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 387 HIS 0.004 0.001 HIS B 91 PHE 0.008 0.001 PHE R 362 TYR 0.007 0.001 TYR R 195 ARG 0.004 0.000 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7539 (p) cc_final: 0.7168 (m) REVERT: A 243 MET cc_start: 0.8027 (tpp) cc_final: 0.7650 (tpt) REVERT: A 294 ASN cc_start: 0.6987 (m-40) cc_final: 0.6702 (t0) REVERT: A 318 GLU cc_start: 0.7206 (mt-10) cc_final: 0.7001 (mt-10) REVERT: G 21 MET cc_start: 0.7100 (mmm) cc_final: 0.6347 (tpt) REVERT: R 65 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7259 (ttm170) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 2.6157 time to fit residues: 421.6797 Evaluate side-chains 105 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 186 GLN R 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9023 Z= 0.160 Angle : 0.545 11.114 12243 Z= 0.269 Chirality : 0.041 0.325 1399 Planarity : 0.005 0.072 1502 Dihedral : 9.082 156.108 1567 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 8.87 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 1080 helix: 2.76 (0.28), residues: 366 sheet: 1.26 (0.32), residues: 278 loop : 0.05 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.002 0.001 HIS B 225 PHE 0.019 0.001 PHE B 292 TYR 0.011 0.001 TYR B 124 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7167 (p) cc_final: 0.6932 (m) REVERT: A 242 ARG cc_start: 0.6563 (mtm-85) cc_final: 0.6345 (mtm-85) REVERT: A 243 MET cc_start: 0.8225 (tpp) cc_final: 0.7547 (tpt) REVERT: A 294 ASN cc_start: 0.7079 (m-40) cc_final: 0.6731 (t0) REVERT: B 19 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5840 (ttm110) REVERT: E 188 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8807 (tp) REVERT: G 21 MET cc_start: 0.7094 (mmm) cc_final: 0.6496 (tpt) REVERT: R 65 ARG cc_start: 0.7529 (ttm170) cc_final: 0.7235 (ttm170) REVERT: R 351 MET cc_start: 0.7495 (mmm) cc_final: 0.7290 (tpt) outliers start: 12 outliers final: 4 residues processed: 126 average time/residue: 2.7756 time to fit residues: 372.8256 Evaluate side-chains 116 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 340 ASN E 186 GLN R 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9023 Z= 0.167 Angle : 0.522 11.811 12243 Z= 0.258 Chirality : 0.040 0.254 1399 Planarity : 0.004 0.047 1502 Dihedral : 8.805 164.343 1567 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.18 % Allowed : 11.32 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1080 helix: 2.50 (0.29), residues: 365 sheet: 1.14 (0.32), residues: 273 loop : -0.05 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.020 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.003 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.6666 (mtm-85) cc_final: 0.6458 (mtm-85) REVERT: A 243 MET cc_start: 0.8216 (tpp) cc_final: 0.7618 (tpt) REVERT: A 294 ASN cc_start: 0.7184 (m-40) cc_final: 0.6780 (t0) REVERT: E 93 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7270 (ttt) REVERT: G 21 MET cc_start: 0.7111 (mmm) cc_final: 0.6586 (tpt) outliers start: 11 outliers final: 6 residues processed: 128 average time/residue: 2.7014 time to fit residues: 368.5814 Evaluate side-chains 121 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.0170 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN E 186 GLN R 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9023 Z= 0.186 Angle : 0.537 11.736 12243 Z= 0.269 Chirality : 0.040 0.201 1399 Planarity : 0.004 0.061 1502 Dihedral : 8.778 160.504 1567 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.03 % Allowed : 11.54 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1080 helix: 2.34 (0.29), residues: 371 sheet: 1.03 (0.32), residues: 261 loop : -0.14 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 322 PHE 0.020 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.6261 (ttpp) cc_final: 0.5790 (tptp) REVERT: E 153 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6148 (tp30) REVERT: G 21 MET cc_start: 0.7031 (mmm) cc_final: 0.6562 (tpt) outliers start: 19 outliers final: 8 residues processed: 126 average time/residue: 2.6127 time to fit residues: 352.1458 Evaluate side-chains 117 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9023 Z= 0.195 Angle : 0.538 11.728 12243 Z= 0.270 Chirality : 0.040 0.221 1399 Planarity : 0.004 0.055 1502 Dihedral : 8.873 161.844 1567 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 11.65 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1080 helix: 2.21 (0.28), residues: 375 sheet: 0.86 (0.32), residues: 260 loop : -0.18 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: G 21 MET cc_start: 0.6997 (mmm) cc_final: 0.6479 (tpt) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 2.5595 time to fit residues: 321.3754 Evaluate side-chains 116 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 0.0070 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 36 GLN R 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9023 Z= 0.159 Angle : 0.520 11.826 12243 Z= 0.259 Chirality : 0.039 0.213 1399 Planarity : 0.004 0.061 1502 Dihedral : 8.714 160.828 1567 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.85 % Allowed : 13.57 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1080 helix: 2.31 (0.28), residues: 375 sheet: 0.73 (0.31), residues: 261 loop : -0.17 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 387 HIS 0.002 0.001 HIS E 35 PHE 0.019 0.001 PHE B 292 TYR 0.012 0.001 TYR R 198 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.6111 (ttpp) cc_final: 0.5639 (tptp) REVERT: B 263 THR cc_start: 0.7966 (t) cc_final: 0.7677 (m) REVERT: G 21 MET cc_start: 0.6964 (mmm) cc_final: 0.6488 (tpt) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 2.5322 time to fit residues: 314.6463 Evaluate side-chains 112 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 64 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9023 Z= 0.187 Angle : 0.535 11.780 12243 Z= 0.268 Chirality : 0.040 0.220 1399 Planarity : 0.004 0.038 1502 Dihedral : 8.850 161.501 1567 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.60 % Allowed : 13.46 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1080 helix: 2.21 (0.28), residues: 375 sheet: 0.69 (0.31), residues: 260 loop : -0.25 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 36 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE B 292 TYR 0.014 0.001 TYR R 198 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 THR cc_start: 0.8124 (t) cc_final: 0.7844 (m) REVERT: E 153 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6250 (mp0) REVERT: G 20 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5262 (ptpt) REVERT: G 21 MET cc_start: 0.6933 (mmm) cc_final: 0.6581 (tpt) outliers start: 15 outliers final: 8 residues processed: 120 average time/residue: 2.4020 time to fit residues: 309.5537 Evaluate side-chains 119 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9023 Z= 0.180 Angle : 0.537 11.785 12243 Z= 0.268 Chirality : 0.040 0.217 1399 Planarity : 0.004 0.040 1502 Dihedral : 8.799 161.473 1567 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.28 % Allowed : 14.00 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1080 helix: 2.21 (0.28), residues: 375 sheet: 0.72 (0.31), residues: 257 loop : -0.31 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 99 HIS 0.003 0.001 HIS B 91 PHE 0.021 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.6151 (ttm110) REVERT: B 263 THR cc_start: 0.8128 (t) cc_final: 0.7869 (m) REVERT: E 153 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6291 (mp0) REVERT: G 20 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5295 (ptpt) REVERT: G 21 MET cc_start: 0.6908 (mmm) cc_final: 0.6579 (tpt) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 2.6374 time to fit residues: 334.9959 Evaluate side-chains 118 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9023 Z= 0.175 Angle : 0.531 11.796 12243 Z= 0.266 Chirality : 0.040 0.219 1399 Planarity : 0.004 0.039 1502 Dihedral : 8.720 161.366 1567 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.28 % Allowed : 14.21 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1080 helix: 2.15 (0.28), residues: 380 sheet: 0.73 (0.31), residues: 257 loop : -0.26 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 387 HIS 0.002 0.001 HIS A 244 PHE 0.022 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.005 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.6188 (ttm110) REVERT: B 263 THR cc_start: 0.8140 (t) cc_final: 0.7901 (m) REVERT: G 20 LYS cc_start: 0.5678 (OUTLIER) cc_final: 0.5265 (ptpt) REVERT: G 21 MET cc_start: 0.6923 (mmm) cc_final: 0.6610 (tpt) REVERT: R 335 MET cc_start: 0.6886 (mtt) cc_final: 0.6577 (ttp) outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 2.5804 time to fit residues: 323.6358 Evaluate side-chains 116 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 406 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9023 Z= 0.319 Angle : 0.630 11.551 12243 Z= 0.322 Chirality : 0.043 0.251 1399 Planarity : 0.006 0.058 1502 Dihedral : 9.559 163.411 1567 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.50 % Allowed : 14.32 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1080 helix: 1.64 (0.27), residues: 380 sheet: 0.64 (0.31), residues: 252 loop : -0.51 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE B 292 TYR 0.022 0.002 TYR B 105 ARG 0.007 0.001 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 THR cc_start: 0.8117 (t) cc_final: 0.7891 (m) REVERT: G 20 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5245 (ptpt) REVERT: G 21 MET cc_start: 0.6908 (mmm) cc_final: 0.6414 (tpt) outliers start: 14 outliers final: 8 residues processed: 115 average time/residue: 2.7716 time to fit residues: 339.8668 Evaluate side-chains 113 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 351 MET Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110355 restraints weight = 31446.573| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.80 r_work: 0.3083 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9023 Z= 0.182 Angle : 0.551 11.870 12243 Z= 0.277 Chirality : 0.040 0.226 1399 Planarity : 0.004 0.043 1502 Dihedral : 9.053 161.288 1567 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.85 % Allowed : 15.28 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1080 helix: 1.93 (0.28), residues: 380 sheet: 0.49 (0.31), residues: 260 loop : -0.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.002 0.001 HIS B 91 PHE 0.024 0.001 PHE B 292 TYR 0.013 0.001 TYR R 198 ARG 0.007 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6886.06 seconds wall clock time: 122 minutes 45.51 seconds (7365.51 seconds total)