Starting phenix.real_space_refine on Fri Feb 16 12:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0j_21000/02_2024/6v0j_21000.pdb" } resolution = 3.78 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 9642 2.51 5 N 2580 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "D" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "E" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "F" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Time building chain proxies: 8.21, per 1000 atoms: 0.54 Number of scatterers: 15252 At special positions: 0 Unit cell: (113.97, 116.59, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2988 8.00 N 2580 7.00 C 9642 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: 6.13 Conformation dependent library (CDL) restraints added in 3.2 seconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 18 sheets defined 12.9% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.630A pdb=" N VAL A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 removed outlier: 3.662A pdb=" N THR A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 361' Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 361' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 122 through 128 removed outlier: 3.668A pdb=" N VAL C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 removed outlier: 4.549A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.615A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.355A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 361' Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.523A pdb=" N ALA D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR D 212 " --> pdb=" O ARG D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.752A pdb=" N LEU D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.168A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 361' Processing helix chain 'E' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 212 removed outlier: 3.662A pdb=" N THR E 212 " --> pdb=" O ARG E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 212' Processing helix chain 'E' and resid 242 through 249 removed outlier: 3.753A pdb=" N LEU E 246 " --> pdb=" O SER E 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.570A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.166A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 361' Processing helix chain 'F' and resid 95 through 102 removed outlier: 3.524A pdb=" N ALA F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 removed outlier: 3.631A pdb=" N VAL F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 212 removed outlier: 3.661A pdb=" N THR F 212 " --> pdb=" O ARG F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 209 through 212' Processing helix chain 'F' and resid 242 through 249 removed outlier: 3.752A pdb=" N LEU F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.571A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.167A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 359 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 354 through 361' Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP A 109 " --> pdb=" O GLY A 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 131 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 134 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 87 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 88 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE A 163 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 220 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG A 340 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.536A pdb=" N TRP B 109 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 131 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET B 134 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 87 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 88 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE B 163 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG B 220 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG B 340 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 3.539A pdb=" N TRP C 109 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 131 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 134 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS C 87 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 88 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.144A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 220 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.569A pdb=" N ARG C 340 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 3.536A pdb=" N TRP D 109 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR D 131 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET D 134 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU D 81 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS D 87 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 88 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 161 through 167 removed outlier: 3.517A pdb=" N ILE D 163 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 220 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 340 through 344 removed outlier: 3.669A pdb=" N ARG D 340 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP E 109 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR E 131 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET E 134 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU E 81 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS E 87 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 88 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 167 removed outlier: 3.516A pdb=" N ILE E 163 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG E 220 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG E 340 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 320 " --> pdb=" O ASN E 316 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 107 through 111 removed outlier: 3.537A pdb=" N TRP F 109 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 131 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET F 134 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU F 81 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS F 87 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 88 " --> pdb=" O PHE F 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 161 through 167 removed outlier: 3.517A pdb=" N ILE F 163 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 220 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 340 through 344 removed outlier: 3.670A pdb=" N ARG F 340 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1050 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: 5.10 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5076 1.34 - 1.46: 2389 1.46 - 1.57: 7943 1.57 - 1.69: 6 1.69 - 1.81: 84 Bond restraints: 15498 Sorted by residual: bond pdb=" CA ARG C 63 " pdb=" CB ARG C 63 " ideal model delta sigma weight residual 1.531 1.611 -0.080 3.28e-02 9.30e+02 6.02e+00 bond pdb=" CA ARG E 63 " pdb=" CB ARG E 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.70e+00 bond pdb=" CA ARG F 63 " pdb=" CB ARG F 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.67e+00 bond pdb=" CA ARG A 63 " pdb=" CB ARG A 63 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.67e+00 bond pdb=" CA ARG B 63 " pdb=" CB ARG B 63 " ideal model delta sigma weight residual 1.531 1.601 -0.071 3.28e-02 9.30e+02 4.63e+00 ... (remaining 15493 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.01: 336 105.01 - 112.24: 7893 112.24 - 119.48: 5041 119.48 - 126.71: 7568 126.71 - 133.94: 162 Bond angle restraints: 21000 Sorted by residual: angle pdb=" C SER D 82 " pdb=" N ASP D 83 " pdb=" CA ASP D 83 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C SER B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C SER E 82 " pdb=" N ASP E 83 " pdb=" CA ASP E 83 " ideal model delta sigma weight residual 121.54 131.16 -9.62 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C SER A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 131.15 -9.61 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C SER F 82 " pdb=" N ASP F 83 " pdb=" CA ASP F 83 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 ... (remaining 20995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 9012 15.07 - 30.15: 308 30.15 - 45.22: 70 45.22 - 60.29: 12 60.29 - 75.36: 30 Dihedral angle restraints: 9432 sinusoidal: 3756 harmonic: 5676 Sorted by residual: dihedral pdb=" CA GLU C 263 " pdb=" C GLU C 263 " pdb=" N ALA C 264 " pdb=" CA ALA C 264 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU D 263 " pdb=" C GLU D 263 " pdb=" N ALA D 264 " pdb=" CA ALA D 264 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N ALA A 264 " pdb=" CA ALA A 264 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1632 0.047 - 0.094: 577 0.094 - 0.141: 203 0.141 - 0.188: 24 0.188 - 0.235: 12 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CA ASP F 83 " pdb=" N ASP F 83 " pdb=" C ASP F 83 " pdb=" CB ASP F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASP A 83 " pdb=" N ASP A 83 " pdb=" C ASP A 83 " pdb=" CB ASP A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP E 83 " pdb=" N ASP E 83 " pdb=" C ASP E 83 " pdb=" CB ASP E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2445 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 120 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C VAL C 120 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL C 120 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 328 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO B 329 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 328 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO E 329 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " -0.034 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5324 2.88 - 3.38: 13381 3.38 - 3.89: 24235 3.89 - 4.39: 25658 4.39 - 4.90: 45484 Nonbonded interactions: 114082 Sorted by model distance: nonbonded pdb=" NH1 ARG E 220 " pdb=" OH TYR E 271 " model vdw 2.373 2.520 nonbonded pdb=" NH1 ARG A 220 " pdb=" OH TYR A 271 " model vdw 2.373 2.520 nonbonded pdb=" NH1 ARG D 220 " pdb=" OH TYR D 271 " model vdw 2.373 2.520 nonbonded pdb=" NH1 ARG F 220 " pdb=" OH TYR F 271 " model vdw 2.373 2.520 nonbonded pdb=" NH1 ARG B 220 " pdb=" OH TYR B 271 " model vdw 2.374 2.520 ... (remaining 114077 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.000 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.570 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.100 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15498 Z= 0.394 Angle : 0.878 11.352 21000 Z= 0.471 Chirality : 0.055 0.235 2448 Planarity : 0.006 0.062 2736 Dihedral : 10.190 75.363 5808 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.76 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.15), residues: 1998 helix: -4.19 (0.25), residues: 72 sheet: -1.86 (0.18), residues: 624 loop : -2.26 (0.13), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.003 0.001 HIS E 276 PHE 0.037 0.003 PHE C 253 TYR 0.015 0.002 TYR C 131 ARG 0.005 0.001 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8768 (mm-40) REVERT: A 142 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8518 (tp-100) REVERT: A 151 GLN cc_start: 0.8981 (tt0) cc_final: 0.8480 (tm-30) REVERT: B 98 MET cc_start: 0.9092 (tpp) cc_final: 0.8816 (tpt) REVERT: B 132 ILE cc_start: 0.9316 (pt) cc_final: 0.8887 (mp) REVERT: B 151 GLN cc_start: 0.8989 (tt0) cc_final: 0.8700 (tm-30) REVERT: B 273 ASP cc_start: 0.8371 (t0) cc_final: 0.7923 (t0) REVERT: B 362 LYS cc_start: 0.9289 (mmtp) cc_final: 0.9068 (tppt) REVERT: C 77 GLN cc_start: 0.8707 (mm110) cc_final: 0.8043 (mm110) REVERT: C 98 MET cc_start: 0.9043 (tpp) cc_final: 0.8651 (tpt) REVERT: C 132 ILE cc_start: 0.9380 (pt) cc_final: 0.9148 (mp) REVERT: C 134 MET cc_start: 0.8410 (ptm) cc_final: 0.8108 (ptt) REVERT: C 151 GLN cc_start: 0.9097 (tt0) cc_final: 0.8795 (tm-30) REVERT: C 161 LEU cc_start: 0.9192 (tp) cc_final: 0.8745 (tt) REVERT: C 273 ASP cc_start: 0.8110 (t0) cc_final: 0.7794 (t0) REVERT: C 359 LEU cc_start: 0.9184 (mm) cc_final: 0.8969 (mt) REVERT: C 362 LYS cc_start: 0.9209 (mmtp) cc_final: 0.8896 (tppt) REVERT: D 142 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8488 (tp-100) REVERT: D 151 GLN cc_start: 0.9073 (tt0) cc_final: 0.8807 (tm-30) REVERT: D 161 LEU cc_start: 0.9163 (tp) cc_final: 0.8961 (tp) REVERT: D 273 ASP cc_start: 0.8202 (t0) cc_final: 0.7951 (t0) REVERT: D 376 GLU cc_start: 0.8775 (pt0) cc_final: 0.8535 (pp20) REVERT: E 69 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8710 (mm110) REVERT: E 72 GLU cc_start: 0.8837 (tt0) cc_final: 0.8630 (tm-30) REVERT: E 77 GLN cc_start: 0.8721 (mm110) cc_final: 0.8146 (mm110) REVERT: E 91 LYS cc_start: 0.9535 (mttt) cc_final: 0.9123 (mtmm) REVERT: E 98 MET cc_start: 0.9231 (tpp) cc_final: 0.8989 (tpt) REVERT: E 138 LYS cc_start: 0.9047 (mttt) cc_final: 0.8579 (mmmt) REVERT: E 151 GLN cc_start: 0.9094 (tt0) cc_final: 0.8676 (tm-30) REVERT: E 273 ASP cc_start: 0.8417 (t0) cc_final: 0.8045 (t0) REVERT: E 362 LYS cc_start: 0.9272 (mmtp) cc_final: 0.9000 (tppt) REVERT: F 77 GLN cc_start: 0.8720 (mm110) cc_final: 0.8178 (mm110) REVERT: F 151 GLN cc_start: 0.9179 (tt0) cc_final: 0.8890 (tm-30) REVERT: F 273 ASP cc_start: 0.8264 (t0) cc_final: 0.7983 (t0) REVERT: F 362 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8853 (tppt) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3181 time to fit residues: 201.2270 Evaluate side-chains 240 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 179 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 164 HIS A 316 ASN B 47 ASN B 316 ASN B 345 ASN C 47 ASN C 345 ASN C 354 ASN D 47 ASN D 164 HIS D 345 ASN E 47 ASN E 345 ASN F 47 ASN F 69 GLN F 164 HIS F 316 ASN F 345 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15498 Z= 0.247 Angle : 0.657 7.611 21000 Z= 0.343 Chirality : 0.047 0.176 2448 Planarity : 0.005 0.045 2736 Dihedral : 5.133 17.792 2136 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.30 % Allowed : 10.32 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 1998 helix: -1.08 (0.56), residues: 72 sheet: -1.50 (0.19), residues: 636 loop : -1.87 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.003 0.001 HIS A 276 PHE 0.014 0.002 PHE C 221 TYR 0.013 0.001 TYR A 154 ARG 0.008 0.001 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 273 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8687 (mm-40) REVERT: A 98 MET cc_start: 0.8835 (mmm) cc_final: 0.8104 (tpt) REVERT: A 151 GLN cc_start: 0.8872 (tt0) cc_final: 0.8548 (tm-30) REVERT: A 316 ASN cc_start: 0.9106 (m110) cc_final: 0.8744 (m110) REVERT: A 355 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8555 (pp) REVERT: B 151 GLN cc_start: 0.8953 (tt0) cc_final: 0.8711 (tm-30) REVERT: B 170 LEU cc_start: 0.9546 (tp) cc_final: 0.9316 (tp) REVERT: B 224 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6706 (m) REVERT: B 273 ASP cc_start: 0.8295 (t0) cc_final: 0.7951 (t0) REVERT: B 316 ASN cc_start: 0.8890 (m110) cc_final: 0.8622 (m110) REVERT: B 362 LYS cc_start: 0.9207 (mmtp) cc_final: 0.8858 (tppt) REVERT: C 77 GLN cc_start: 0.8639 (mm110) cc_final: 0.8003 (mm110) REVERT: C 98 MET cc_start: 0.9067 (tpp) cc_final: 0.8425 (tpt) REVERT: C 132 ILE cc_start: 0.9406 (pt) cc_final: 0.9042 (mt) REVERT: C 151 GLN cc_start: 0.9065 (tt0) cc_final: 0.8854 (tm-30) REVERT: C 224 VAL cc_start: 0.6961 (OUTLIER) cc_final: 0.6609 (m) REVERT: C 273 ASP cc_start: 0.8144 (t0) cc_final: 0.7878 (t0) REVERT: C 303 GLN cc_start: 0.9066 (mp10) cc_final: 0.8830 (mp10) REVERT: C 362 LYS cc_start: 0.9215 (mmtp) cc_final: 0.8885 (tppt) REVERT: C 376 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: D 54 MET cc_start: 0.7672 (mmp) cc_final: 0.7332 (mmp) REVERT: D 77 GLN cc_start: 0.8421 (mm110) cc_final: 0.8139 (mm110) REVERT: D 85 LEU cc_start: 0.8924 (tp) cc_final: 0.8503 (mt) REVERT: D 98 MET cc_start: 0.8786 (mmm) cc_final: 0.8356 (tpt) REVERT: E 54 MET cc_start: 0.7647 (mmp) cc_final: 0.7364 (tpp) REVERT: E 77 GLN cc_start: 0.8652 (mm110) cc_final: 0.8119 (mm110) REVERT: E 85 LEU cc_start: 0.8883 (tp) cc_final: 0.8523 (mt) REVERT: E 91 LYS cc_start: 0.9585 (mttt) cc_final: 0.9202 (mtmm) REVERT: E 98 MET cc_start: 0.9207 (tpp) cc_final: 0.8980 (tpt) REVERT: E 105 GLU cc_start: 0.9049 (tp30) cc_final: 0.8597 (mm-30) REVERT: E 151 GLN cc_start: 0.9026 (tt0) cc_final: 0.8749 (tm-30) REVERT: E 170 LEU cc_start: 0.9532 (tp) cc_final: 0.9321 (tp) REVERT: E 224 VAL cc_start: 0.7289 (OUTLIER) cc_final: 0.6920 (m) REVERT: E 273 ASP cc_start: 0.8342 (t0) cc_final: 0.8049 (t0) REVERT: F 63 ARG cc_start: 0.7835 (ppt170) cc_final: 0.7477 (ppt170) REVERT: F 77 GLN cc_start: 0.8619 (mm110) cc_final: 0.8249 (mm110) REVERT: F 98 MET cc_start: 0.8968 (mmm) cc_final: 0.8419 (tpt) REVERT: F 151 GLN cc_start: 0.9106 (tt0) cc_final: 0.8865 (tm-30) REVERT: F 224 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6625 (m) REVERT: F 273 ASP cc_start: 0.8098 (t0) cc_final: 0.7853 (t0) REVERT: F 303 GLN cc_start: 0.9067 (mp10) cc_final: 0.8848 (mp10) REVERT: F 309 GLN cc_start: 0.8673 (tp40) cc_final: 0.8412 (tp40) REVERT: F 316 ASN cc_start: 0.9013 (m110) cc_final: 0.8724 (m110) REVERT: F 320 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8712 (mmmm) REVERT: F 356 SER cc_start: 0.9375 (m) cc_final: 0.9125 (p) REVERT: F 362 LYS cc_start: 0.9096 (mmtp) cc_final: 0.8839 (tppt) outliers start: 22 outliers final: 4 residues processed: 287 average time/residue: 0.3202 time to fit residues: 131.1517 Evaluate side-chains 219 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 122 optimal weight: 0.0570 chunk 49 optimal weight: 0.3980 chunk 180 optimal weight: 0.0070 chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN F 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15498 Z= 0.156 Angle : 0.584 9.992 21000 Z= 0.304 Chirality : 0.045 0.150 2448 Planarity : 0.004 0.041 2736 Dihedral : 4.601 16.732 2136 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.02 % Allowed : 10.08 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.17), residues: 1998 helix: -0.38 (0.63), residues: 72 sheet: -1.24 (0.19), residues: 624 loop : -1.69 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 222 HIS 0.002 0.000 HIS D 276 PHE 0.012 0.001 PHE C 253 TYR 0.014 0.001 TYR D 154 ARG 0.005 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8892 (mmm) cc_final: 0.8214 (tpt) REVERT: A 151 GLN cc_start: 0.8920 (tt0) cc_final: 0.8593 (tm-30) REVERT: A 355 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8541 (pp) REVERT: B 151 GLN cc_start: 0.8934 (tt0) cc_final: 0.8652 (tm-30) REVERT: B 224 VAL cc_start: 0.7225 (OUTLIER) cc_final: 0.6877 (m) REVERT: B 273 ASP cc_start: 0.8254 (t0) cc_final: 0.7954 (t0) REVERT: B 316 ASN cc_start: 0.8915 (m110) cc_final: 0.8710 (m110) REVERT: C 54 MET cc_start: 0.8127 (mmp) cc_final: 0.7895 (mmp) REVERT: C 85 LEU cc_start: 0.8998 (tp) cc_final: 0.8761 (tp) REVERT: C 132 ILE cc_start: 0.9349 (pt) cc_final: 0.8984 (mt) REVERT: C 142 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8654 (tp-100) REVERT: C 224 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6587 (m) REVERT: C 273 ASP cc_start: 0.8134 (t0) cc_final: 0.7891 (t0) REVERT: C 302 TYR cc_start: 0.9272 (t80) cc_final: 0.8637 (t80) REVERT: C 303 GLN cc_start: 0.9014 (mp10) cc_final: 0.8593 (mp10) REVERT: C 362 LYS cc_start: 0.9177 (mmtp) cc_final: 0.8807 (tppt) REVERT: C 376 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: D 54 MET cc_start: 0.7834 (mmp) cc_final: 0.7441 (mmp) REVERT: D 77 GLN cc_start: 0.8509 (mm110) cc_final: 0.8224 (mp10) REVERT: D 98 MET cc_start: 0.8793 (mmm) cc_final: 0.8342 (tpt) REVERT: D 151 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 309 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8365 (tp40) REVERT: E 54 MET cc_start: 0.7801 (mmp) cc_final: 0.7403 (tpp) REVERT: E 85 LEU cc_start: 0.8799 (tp) cc_final: 0.8578 (tp) REVERT: E 91 LYS cc_start: 0.9556 (mttt) cc_final: 0.9223 (mtmm) REVERT: E 151 GLN cc_start: 0.9021 (tt0) cc_final: 0.8770 (tm-30) REVERT: E 224 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.6966 (m) REVERT: E 273 ASP cc_start: 0.8298 (t0) cc_final: 0.8029 (t0) REVERT: E 362 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8857 (tppt) REVERT: F 54 MET cc_start: 0.8192 (mmp) cc_final: 0.7906 (mmp) REVERT: F 98 MET cc_start: 0.8749 (mmm) cc_final: 0.8295 (tpt) REVERT: F 132 ILE cc_start: 0.9276 (pt) cc_final: 0.9035 (mt) REVERT: F 142 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8487 (tp-100) REVERT: F 151 GLN cc_start: 0.9112 (tt0) cc_final: 0.8908 (tm-30) REVERT: F 224 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6587 (m) REVERT: F 303 GLN cc_start: 0.9064 (mp10) cc_final: 0.8839 (mp10) REVERT: F 309 GLN cc_start: 0.8622 (tp40) cc_final: 0.8371 (tp40) REVERT: F 320 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8681 (mmmm) REVERT: F 356 SER cc_start: 0.9421 (m) cc_final: 0.9173 (p) REVERT: F 362 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8831 (tppt) outliers start: 34 outliers final: 9 residues processed: 278 average time/residue: 0.2910 time to fit residues: 116.1479 Evaluate side-chains 224 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 85 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.0070 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15498 Z= 0.168 Angle : 0.570 9.937 21000 Z= 0.297 Chirality : 0.045 0.154 2448 Planarity : 0.004 0.039 2736 Dihedral : 4.439 16.914 2136 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.14 % Allowed : 12.04 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 1998 helix: -0.16 (0.65), residues: 72 sheet: -0.92 (0.20), residues: 612 loop : -1.53 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 222 HIS 0.002 0.001 HIS F 276 PHE 0.018 0.001 PHE B 377 TYR 0.026 0.001 TYR B 302 ARG 0.005 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 229 time to evaluate : 1.919 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: A 69 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8983 (mm-40) REVERT: A 98 MET cc_start: 0.8707 (mmm) cc_final: 0.8347 (tpt) REVERT: A 355 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8604 (pp) REVERT: B 63 ARG cc_start: 0.7894 (ppt170) cc_final: 0.7581 (ppt170) REVERT: B 151 GLN cc_start: 0.8935 (tt0) cc_final: 0.8665 (tm-30) REVERT: B 195 ASN cc_start: 0.9534 (OUTLIER) cc_final: 0.9323 (p0) REVERT: B 224 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7004 (m) REVERT: B 273 ASP cc_start: 0.8231 (t0) cc_final: 0.7962 (t0) REVERT: B 309 GLN cc_start: 0.8630 (tp40) cc_final: 0.8399 (tp40) REVERT: C 85 LEU cc_start: 0.8982 (tp) cc_final: 0.8737 (tp) REVERT: C 132 ILE cc_start: 0.9323 (pt) cc_final: 0.9037 (mp) REVERT: C 142 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8717 (tp-100) REVERT: C 224 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6706 (m) REVERT: C 273 ASP cc_start: 0.8151 (t0) cc_final: 0.7906 (t0) REVERT: C 362 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8770 (tppt) REVERT: C 376 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: D 54 MET cc_start: 0.7782 (mmp) cc_final: 0.7553 (mmp) REVERT: D 69 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8755 (mp10) REVERT: D 77 GLN cc_start: 0.8491 (mm110) cc_final: 0.8239 (mp10) REVERT: D 98 MET cc_start: 0.8802 (mmm) cc_final: 0.8426 (tpt) REVERT: D 195 ASN cc_start: 0.9365 (OUTLIER) cc_final: 0.9085 (p0) REVERT: D 197 ASN cc_start: 0.8606 (t0) cc_final: 0.8262 (t0) REVERT: D 309 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8493 (tp40) REVERT: E 54 MET cc_start: 0.7833 (mmp) cc_final: 0.7557 (mmp) REVERT: E 63 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7800 (ppt170) REVERT: E 85 LEU cc_start: 0.8750 (tp) cc_final: 0.8528 (tp) REVERT: E 91 LYS cc_start: 0.9580 (mttt) cc_final: 0.9048 (ptpp) REVERT: E 151 GLN cc_start: 0.9012 (tt0) cc_final: 0.8776 (tm-30) REVERT: E 195 ASN cc_start: 0.9431 (OUTLIER) cc_final: 0.9210 (p0) REVERT: E 224 VAL cc_start: 0.7332 (OUTLIER) cc_final: 0.7003 (m) REVERT: E 273 ASP cc_start: 0.8245 (t0) cc_final: 0.8027 (t0) REVERT: E 302 TYR cc_start: 0.9165 (t80) cc_final: 0.8919 (t80) REVERT: F 98 MET cc_start: 0.8837 (mmm) cc_final: 0.8583 (tpt) REVERT: F 132 ILE cc_start: 0.9258 (pt) cc_final: 0.9015 (mt) REVERT: F 142 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8490 (tp-100) REVERT: F 151 GLN cc_start: 0.9110 (tt0) cc_final: 0.8902 (tm-30) REVERT: F 224 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6671 (m) REVERT: F 303 GLN cc_start: 0.9069 (mp10) cc_final: 0.8814 (mp10) REVERT: F 309 GLN cc_start: 0.8618 (tp40) cc_final: 0.8353 (tp40) REVERT: F 355 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8438 (pp) REVERT: F 362 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8790 (tppt) outliers start: 36 outliers final: 14 residues processed: 257 average time/residue: 0.3324 time to fit residues: 122.4330 Evaluate side-chains 223 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15498 Z= 0.428 Angle : 0.707 10.395 21000 Z= 0.363 Chirality : 0.048 0.161 2448 Planarity : 0.005 0.040 2736 Dihedral : 5.124 17.492 2136 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.14 % Allowed : 13.64 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 1998 helix: -0.26 (0.66), residues: 72 sheet: -0.99 (0.20), residues: 612 loop : -1.48 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.004 0.001 HIS E 276 PHE 0.011 0.002 PHE A 145 TYR 0.030 0.002 TYR C 302 ARG 0.006 0.001 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8936 (mm-40) REVERT: A 98 MET cc_start: 0.8706 (mmm) cc_final: 0.8221 (tpt) REVERT: A 151 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 355 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8567 (pp) REVERT: B 63 ARG cc_start: 0.8021 (ppt170) cc_final: 0.7768 (ppt170) REVERT: B 151 GLN cc_start: 0.9037 (tt0) cc_final: 0.8757 (tm-30) REVERT: B 224 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7070 (m) REVERT: B 273 ASP cc_start: 0.8468 (t0) cc_final: 0.8116 (t0) REVERT: B 309 GLN cc_start: 0.8733 (tp40) cc_final: 0.8445 (tp40) REVERT: C 54 MET cc_start: 0.8057 (mmp) cc_final: 0.7826 (tpp) REVERT: C 98 MET cc_start: 0.8867 (mmm) cc_final: 0.8379 (tpt) REVERT: C 142 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8894 (tp-100) REVERT: C 224 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.7050 (m) REVERT: C 303 GLN cc_start: 0.9065 (mp10) cc_final: 0.8647 (mp10) REVERT: D 54 MET cc_start: 0.7751 (mmp) cc_final: 0.7306 (mmp) REVERT: D 98 MET cc_start: 0.8816 (mmm) cc_final: 0.8461 (tpt) REVERT: D 151 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8059 (tm-30) REVERT: D 309 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8361 (tp40) REVERT: D 359 LEU cc_start: 0.9384 (mm) cc_final: 0.9083 (mp) REVERT: E 54 MET cc_start: 0.7840 (mmp) cc_final: 0.7496 (mmp) REVERT: E 63 ARG cc_start: 0.8047 (ppt170) cc_final: 0.7566 (ppt170) REVERT: E 69 GLN cc_start: 0.8913 (mp10) cc_final: 0.8686 (mp10) REVERT: E 151 GLN cc_start: 0.9060 (tt0) cc_final: 0.8705 (tm-30) REVERT: E 166 GLN cc_start: 0.8944 (mt0) cc_final: 0.8652 (mt0) REVERT: E 224 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7120 (m) REVERT: E 273 ASP cc_start: 0.8513 (t0) cc_final: 0.8189 (t0) REVERT: E 309 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8439 (tp40) REVERT: F 151 GLN cc_start: 0.9142 (tt0) cc_final: 0.8855 (tm-30) REVERT: F 224 VAL cc_start: 0.7245 (OUTLIER) cc_final: 0.7008 (m) REVERT: F 303 GLN cc_start: 0.8993 (mp10) cc_final: 0.8693 (mp10) REVERT: F 355 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8509 (pp) REVERT: F 362 LYS cc_start: 0.9145 (mmtp) cc_final: 0.8921 (mmtm) outliers start: 53 outliers final: 24 residues processed: 244 average time/residue: 0.2961 time to fit residues: 104.4616 Evaluate side-chains 207 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.5980 chunk 172 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15498 Z= 0.174 Angle : 0.586 11.545 21000 Z= 0.302 Chirality : 0.046 0.170 2448 Planarity : 0.004 0.040 2736 Dihedral : 4.594 19.122 2136 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.19 % Allowed : 14.77 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 1998 helix: -0.14 (0.67), residues: 72 sheet: -0.71 (0.21), residues: 570 loop : -1.48 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 222 HIS 0.002 0.000 HIS F 276 PHE 0.012 0.001 PHE C 253 TYR 0.022 0.001 TYR E 302 ARG 0.004 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8923 (mm-40) REVERT: A 98 MET cc_start: 0.8854 (mmm) cc_final: 0.8220 (tpt) REVERT: A 151 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 355 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8765 (pp) REVERT: B 63 ARG cc_start: 0.7982 (ppt170) cc_final: 0.7616 (ppt170) REVERT: B 224 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7039 (m) REVERT: B 273 ASP cc_start: 0.8418 (t0) cc_final: 0.8102 (t0) REVERT: B 301 MET cc_start: 0.8594 (mmp) cc_final: 0.8204 (mmm) REVERT: B 309 GLN cc_start: 0.8640 (tp40) cc_final: 0.8396 (tp40) REVERT: C 98 MET cc_start: 0.8609 (mmm) cc_final: 0.8248 (tpt) REVERT: C 142 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8910 (tp-100) REVERT: C 151 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 224 VAL cc_start: 0.7150 (OUTLIER) cc_final: 0.6884 (m) REVERT: C 303 GLN cc_start: 0.9080 (mp10) cc_final: 0.8864 (mp10) REVERT: D 69 GLN cc_start: 0.9231 (mm110) cc_final: 0.8905 (mm-40) REVERT: D 98 MET cc_start: 0.8980 (mmm) cc_final: 0.8697 (tpt) REVERT: D 135 MET cc_start: 0.8900 (mmt) cc_final: 0.8615 (tpp) REVERT: D 309 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8503 (tp40) REVERT: E 54 MET cc_start: 0.7936 (mmp) cc_final: 0.7569 (mmp) REVERT: E 63 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7554 (ppt170) REVERT: E 91 LYS cc_start: 0.9575 (mttt) cc_final: 0.9061 (ptpp) REVERT: E 151 GLN cc_start: 0.9004 (tt0) cc_final: 0.8772 (tm-30) REVERT: E 224 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7118 (m) REVERT: E 273 ASP cc_start: 0.8398 (t0) cc_final: 0.8112 (t0) REVERT: F 132 ILE cc_start: 0.9284 (pt) cc_final: 0.9079 (mt) REVERT: F 224 VAL cc_start: 0.7084 (OUTLIER) cc_final: 0.6812 (m) REVERT: F 362 LYS cc_start: 0.9135 (mmtp) cc_final: 0.8810 (tppt) outliers start: 37 outliers final: 22 residues processed: 236 average time/residue: 0.2897 time to fit residues: 99.2917 Evaluate side-chains 215 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 376 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.0980 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15498 Z= 0.256 Angle : 0.630 12.679 21000 Z= 0.321 Chirality : 0.047 0.178 2448 Planarity : 0.004 0.040 2736 Dihedral : 4.656 20.279 2136 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.79 % Allowed : 15.01 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 1998 helix: -0.24 (0.67), residues: 72 sheet: -0.71 (0.21), residues: 570 loop : -1.43 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 222 HIS 0.002 0.001 HIS F 276 PHE 0.010 0.001 PHE C 253 TYR 0.030 0.002 TYR F 302 ARG 0.007 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 1.932 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: A 69 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8893 (mm-40) REVERT: A 98 MET cc_start: 0.8567 (mmm) cc_final: 0.8345 (tpt) REVERT: A 134 MET cc_start: 0.8416 (ptm) cc_final: 0.8127 (ppp) REVERT: A 151 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 355 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8759 (pp) REVERT: B 63 ARG cc_start: 0.8050 (ppt170) cc_final: 0.7640 (ppt170) REVERT: B 224 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7100 (m) REVERT: B 273 ASP cc_start: 0.8423 (t0) cc_final: 0.8121 (t0) REVERT: B 309 GLN cc_start: 0.8705 (tp40) cc_final: 0.8421 (tp40) REVERT: B 374 ARG cc_start: 0.7515 (ptt90) cc_final: 0.7202 (ptt90) REVERT: C 98 MET cc_start: 0.8916 (mmm) cc_final: 0.8260 (tpt) REVERT: C 151 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 224 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6877 (m) REVERT: C 303 GLN cc_start: 0.9083 (mp10) cc_final: 0.8785 (mp10) REVERT: D 54 MET cc_start: 0.7805 (mmp) cc_final: 0.7373 (mmp) REVERT: D 69 GLN cc_start: 0.9340 (mm110) cc_final: 0.8902 (mm-40) REVERT: D 98 MET cc_start: 0.8941 (mmm) cc_final: 0.8665 (tpt) REVERT: D 151 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8240 (tm-30) REVERT: D 195 ASN cc_start: 0.9448 (OUTLIER) cc_final: 0.9246 (p0) REVERT: D 309 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8383 (tp40) REVERT: D 324 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: D 359 LEU cc_start: 0.9388 (mm) cc_final: 0.9144 (mp) REVERT: E 54 MET cc_start: 0.7891 (mmp) cc_final: 0.7519 (mmp) REVERT: E 63 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7576 (ppt170) REVERT: E 69 GLN cc_start: 0.9015 (mp10) cc_final: 0.8749 (mp10) REVERT: E 91 LYS cc_start: 0.9573 (mttt) cc_final: 0.9079 (ptpp) REVERT: E 151 GLN cc_start: 0.9043 (tt0) cc_final: 0.8721 (tm-30) REVERT: E 224 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7077 (m) REVERT: E 273 ASP cc_start: 0.8432 (t0) cc_final: 0.8136 (t0) REVERT: E 301 MET cc_start: 0.8870 (mmp) cc_final: 0.8543 (mmm) REVERT: F 142 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8827 (tp-100) REVERT: F 224 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6911 (m) outliers start: 47 outliers final: 28 residues processed: 225 average time/residue: 0.2923 time to fit residues: 94.9650 Evaluate side-chains 215 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 316 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.0970 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN C 309 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15498 Z= 0.206 Angle : 0.616 13.554 21000 Z= 0.312 Chirality : 0.046 0.197 2448 Planarity : 0.004 0.039 2736 Dihedral : 4.519 19.486 2136 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.49 % Allowed : 15.48 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 1998 helix: -0.32 (0.66), residues: 72 sheet: -0.66 (0.21), residues: 570 loop : -1.45 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.002 0.000 HIS C 276 PHE 0.011 0.001 PHE C 253 TYR 0.016 0.001 TYR C 302 ARG 0.006 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.910 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: A 69 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8888 (mm-40) REVERT: A 134 MET cc_start: 0.8382 (ptm) cc_final: 0.8153 (ppp) REVERT: A 151 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 355 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8767 (pp) REVERT: B 63 ARG cc_start: 0.8070 (ppt170) cc_final: 0.7655 (ppt170) REVERT: B 224 VAL cc_start: 0.7353 (OUTLIER) cc_final: 0.7059 (m) REVERT: B 273 ASP cc_start: 0.8421 (t0) cc_final: 0.8112 (t0) REVERT: B 301 MET cc_start: 0.8682 (mmp) cc_final: 0.8315 (mmm) REVERT: B 309 GLN cc_start: 0.8666 (tp40) cc_final: 0.8408 (tp40) REVERT: B 374 ARG cc_start: 0.7463 (ptt90) cc_final: 0.7090 (ptt90) REVERT: C 54 MET cc_start: 0.7998 (mmp) cc_final: 0.7797 (tpp) REVERT: C 63 ARG cc_start: 0.7903 (ppt170) cc_final: 0.7484 (ppt170) REVERT: C 98 MET cc_start: 0.8811 (mmm) cc_final: 0.8184 (tpt) REVERT: C 151 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 224 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6890 (m) REVERT: C 303 GLN cc_start: 0.9038 (mp10) cc_final: 0.8677 (mp10) REVERT: C 355 LEU cc_start: 0.9153 (mt) cc_final: 0.8698 (pp) REVERT: D 69 GLN cc_start: 0.9300 (mm110) cc_final: 0.8928 (mm-40) REVERT: D 98 MET cc_start: 0.8894 (mmm) cc_final: 0.8617 (tpt) REVERT: D 151 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 195 ASN cc_start: 0.9442 (OUTLIER) cc_final: 0.9226 (p0) REVERT: D 309 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8495 (tp40) REVERT: D 355 LEU cc_start: 0.9125 (mt) cc_final: 0.8511 (pp) REVERT: D 359 LEU cc_start: 0.9383 (mm) cc_final: 0.9117 (mp) REVERT: E 54 MET cc_start: 0.7932 (mmp) cc_final: 0.7548 (mmp) REVERT: E 63 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7626 (ppt170) REVERT: E 91 LYS cc_start: 0.9575 (mttt) cc_final: 0.9084 (ptpp) REVERT: E 107 GLN cc_start: 0.9541 (mt0) cc_final: 0.9192 (mp10) REVERT: E 151 GLN cc_start: 0.9000 (tt0) cc_final: 0.8765 (tm-30) REVERT: E 224 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7132 (m) REVERT: E 273 ASP cc_start: 0.8414 (t0) cc_final: 0.8116 (t0) REVERT: F 132 ILE cc_start: 0.9289 (pt) cc_final: 0.9087 (mt) REVERT: F 142 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8885 (tp-100) REVERT: F 224 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6848 (m) REVERT: F 309 GLN cc_start: 0.8659 (tp40) cc_final: 0.8356 (tp40) outliers start: 42 outliers final: 29 residues processed: 217 average time/residue: 0.2755 time to fit residues: 87.3599 Evaluate side-chains 219 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 316 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15498 Z= 0.225 Angle : 0.624 11.969 21000 Z= 0.316 Chirality : 0.047 0.174 2448 Planarity : 0.004 0.039 2736 Dihedral : 4.535 21.979 2136 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.49 % Allowed : 15.48 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.17), residues: 1998 helix: -0.34 (0.66), residues: 72 sheet: -0.65 (0.21), residues: 570 loop : -1.46 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 222 HIS 0.002 0.001 HIS F 276 PHE 0.011 0.001 PHE C 253 TYR 0.048 0.001 TYR B 68 ARG 0.004 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8863 (mm-40) REVERT: A 134 MET cc_start: 0.8178 (ptm) cc_final: 0.7972 (ppp) REVERT: A 151 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 355 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 63 ARG cc_start: 0.8091 (ppt170) cc_final: 0.7673 (ppt170) REVERT: B 224 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7073 (m) REVERT: B 237 LYS cc_start: 0.7679 (pttt) cc_final: 0.7442 (mtpp) REVERT: B 273 ASP cc_start: 0.8426 (t0) cc_final: 0.8138 (t0) REVERT: B 301 MET cc_start: 0.8720 (mmp) cc_final: 0.8329 (mmm) REVERT: B 309 GLN cc_start: 0.8657 (tp40) cc_final: 0.8394 (tp40) REVERT: B 374 ARG cc_start: 0.7411 (ptt90) cc_final: 0.7018 (ptt90) REVERT: C 63 ARG cc_start: 0.7880 (ppt170) cc_final: 0.7470 (ppt170) REVERT: C 98 MET cc_start: 0.8816 (mmm) cc_final: 0.8186 (tpt) REVERT: C 105 GLU cc_start: 0.9115 (tp30) cc_final: 0.8734 (mm-30) REVERT: C 151 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8484 (tm-30) REVERT: C 224 VAL cc_start: 0.7121 (OUTLIER) cc_final: 0.6876 (m) REVERT: C 303 GLN cc_start: 0.9045 (mp10) cc_final: 0.8615 (mp10) REVERT: C 355 LEU cc_start: 0.9163 (mt) cc_final: 0.8729 (pp) REVERT: D 54 MET cc_start: 0.7851 (mmp) cc_final: 0.7594 (mmp) REVERT: D 98 MET cc_start: 0.8886 (mmm) cc_final: 0.8624 (tpt) REVERT: D 151 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8303 (tm-30) REVERT: D 195 ASN cc_start: 0.9439 (OUTLIER) cc_final: 0.9237 (p0) REVERT: D 309 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8332 (tp40) REVERT: D 324 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: D 355 LEU cc_start: 0.9135 (mt) cc_final: 0.8525 (pp) REVERT: D 359 LEU cc_start: 0.9350 (mm) cc_final: 0.9084 (mp) REVERT: E 54 MET cc_start: 0.7923 (mmp) cc_final: 0.7533 (mmp) REVERT: E 63 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7590 (ppt170) REVERT: E 91 LYS cc_start: 0.9593 (mttt) cc_final: 0.9077 (ptpp) REVERT: E 107 GLN cc_start: 0.9525 (mt0) cc_final: 0.9144 (mp10) REVERT: E 151 GLN cc_start: 0.9005 (tt0) cc_final: 0.8785 (tm-30) REVERT: E 224 VAL cc_start: 0.7322 (OUTLIER) cc_final: 0.7071 (m) REVERT: E 273 ASP cc_start: 0.8420 (t0) cc_final: 0.8117 (t0) REVERT: E 301 MET cc_start: 0.8832 (mmp) cc_final: 0.8561 (mmm) REVERT: F 63 ARG cc_start: 0.7885 (ppt170) cc_final: 0.7385 (ppt170) REVERT: F 132 ILE cc_start: 0.9295 (pt) cc_final: 0.9093 (mt) REVERT: F 142 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8900 (tp-100) REVERT: F 224 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6893 (m) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 0.2896 time to fit residues: 91.0156 Evaluate side-chains 220 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 154 TYR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 chunk 89 optimal weight: 0.0040 chunk 130 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15498 Z= 0.162 Angle : 0.611 12.204 21000 Z= 0.307 Chirality : 0.046 0.162 2448 Planarity : 0.004 0.039 2736 Dihedral : 4.321 25.686 2136 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.25 % Allowed : 15.54 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 1998 helix: -0.26 (0.67), residues: 72 sheet: -0.62 (0.21), residues: 570 loop : -1.45 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.001 0.000 HIS F 276 PHE 0.011 0.001 PHE C 253 TYR 0.013 0.001 TYR C 302 ARG 0.005 0.000 ARG E 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 197 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8305 (ptm) cc_final: 0.8015 (ppp) REVERT: A 355 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 63 ARG cc_start: 0.8054 (ppt170) cc_final: 0.7684 (ppt170) REVERT: B 151 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 224 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7022 (m) REVERT: B 273 ASP cc_start: 0.8370 (t0) cc_final: 0.8067 (t0) REVERT: B 301 MET cc_start: 0.8623 (mmp) cc_final: 0.8282 (mmm) REVERT: B 309 GLN cc_start: 0.8550 (tp40) cc_final: 0.8328 (tp40) REVERT: B 374 ARG cc_start: 0.7418 (ptt90) cc_final: 0.7123 (ptt90) REVERT: C 63 ARG cc_start: 0.7902 (ppt170) cc_final: 0.7470 (ppt170) REVERT: C 98 MET cc_start: 0.8777 (mmm) cc_final: 0.8080 (tpt) REVERT: C 105 GLU cc_start: 0.9108 (tp30) cc_final: 0.8726 (mm-30) REVERT: C 151 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 224 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6857 (m) REVERT: C 355 LEU cc_start: 0.9013 (mt) cc_final: 0.8733 (pp) REVERT: D 63 ARG cc_start: 0.7853 (ppt170) cc_final: 0.7530 (ppt170) REVERT: D 98 MET cc_start: 0.8912 (mmm) cc_final: 0.8657 (tpt) REVERT: D 151 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 195 ASN cc_start: 0.9396 (OUTLIER) cc_final: 0.9149 (p0) REVERT: D 309 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8481 (tp40) REVERT: D 355 LEU cc_start: 0.9126 (mt) cc_final: 0.8549 (pp) REVERT: D 359 LEU cc_start: 0.9316 (mm) cc_final: 0.9033 (mp) REVERT: E 54 MET cc_start: 0.7955 (mmp) cc_final: 0.7561 (mmp) REVERT: E 63 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7264 (pmt-80) REVERT: E 91 LYS cc_start: 0.9592 (mttt) cc_final: 0.9081 (ptpp) REVERT: E 107 GLN cc_start: 0.9525 (mt0) cc_final: 0.9143 (mp10) REVERT: E 151 GLN cc_start: 0.8996 (tt0) cc_final: 0.8784 (tm-30) REVERT: E 224 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7063 (m) REVERT: E 273 ASP cc_start: 0.8282 (t0) cc_final: 0.8053 (t0) REVERT: E 301 MET cc_start: 0.8741 (mmp) cc_final: 0.8488 (mmm) REVERT: F 63 ARG cc_start: 0.7960 (ppt170) cc_final: 0.7460 (ppt170) REVERT: F 142 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8904 (tp-100) REVERT: F 224 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6811 (m) REVERT: F 309 GLN cc_start: 0.8652 (tp40) cc_final: 0.8379 (tp40) outliers start: 38 outliers final: 24 residues processed: 223 average time/residue: 0.2738 time to fit residues: 89.6583 Evaluate side-chains 211 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 154 TYR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 316 ASN Chi-restraints excluded: chain F residue 350 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081982 restraints weight = 33916.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084911 restraints weight = 19446.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086927 restraints weight = 13460.145| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15498 Z= 0.234 Angle : 0.644 12.324 21000 Z= 0.325 Chirality : 0.047 0.187 2448 Planarity : 0.004 0.039 2736 Dihedral : 4.478 25.865 2136 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.25 % Allowed : 16.07 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 1998 helix: -0.23 (0.67), residues: 72 sheet: -0.61 (0.21), residues: 570 loop : -1.43 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.002 0.001 HIS F 276 PHE 0.011 0.001 PHE C 253 TYR 0.064 0.002 TYR B 68 ARG 0.004 0.000 ARG E 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.43 seconds wall clock time: 57 minutes 43.94 seconds (3463.94 seconds total)