Starting phenix.real_space_refine on Fri Feb 16 12:31:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/02_2024/6v0g_20997.pdb" } resolution = 3.03 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= 0.006 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 86": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 220": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 86": "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: 7.85, per 1000 atoms: 0.51 Number of scatterers: 15252 At special positions: 0 Unit cell: (113.97, 113.97, 103.49, 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: 5.25 Conformation dependent library (CDL) restraints added in 2.9 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: 48 helices and 30 sheets defined 15.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.174A pdb=" N THR A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 86' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 333 removed outlier: 4.174A pdb=" N THR B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 209 through 214 removed outlier: 4.332A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 86' Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 209 through 214 removed outlier: 4.332A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 86' Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR E 333 " --> pdb=" O PRO E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.197A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 86 removed outlier: 3.644A pdb=" N ARG F 86 " --> pdb=" O ASP F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 86' Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 Processing helix chain 'F' and resid 209 through 214 removed outlier: 4.333A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.918A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.672A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.173A pdb=" N THR F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.198A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU A 81 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS A 87 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.527A pdb=" N ALA B 236 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 removed outlier: 3.526A pdb=" N ALA A 236 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU A 324 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 313 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A 315 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS A 320 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.158A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS B 87 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 230 through 231 removed outlier: 3.526A pdb=" N ALA C 236 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU B 324 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 313 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 315 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS B 320 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.158A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS C 87 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 111 Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.526A pdb=" N ALA D 236 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU C 324 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 313 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR C 322 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C 315 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS C 320 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU D 81 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS D 87 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 107 through 111 Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 230 through 231 removed outlier: 3.505A pdb=" N ALA E 236 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.359A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU D 324 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 313 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR D 322 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 315 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS D 320 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU E 81 " --> pdb=" O LYS E 87 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS E 87 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 107 through 111 Processing sheet with id=AC6, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 230 through 231 removed outlier: 3.528A pdb=" N ALA F 236 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.359A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU E 324 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 313 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 322 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU E 315 " --> pdb=" O LYS E 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS E 320 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.159A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU F 81 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS F 87 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 107 through 111 Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.855A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.358A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU F 324 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU F 313 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR F 322 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU F 315 " --> pdb=" O LYS F 320 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS F 320 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1152 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: 5.05 Time building geometry restraints manager: 5.71 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: 4932 1.34 - 1.45: 2018 1.45 - 1.57: 8464 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15498 Sorted by residual: bond pdb=" CB VAL F 201 " pdb=" CG2 VAL F 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL C 201 " pdb=" CG2 VAL C 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL D 201 " pdb=" CG2 VAL D 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB VAL A 201 " pdb=" CG2 VAL A 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB VAL B 201 " pdb=" CG2 VAL B 201 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 15493 not shown) Histogram of bond angle deviations from ideal: 98.73 - 107.73: 798 107.73 - 116.73: 10487 116.73 - 125.73: 9505 125.73 - 134.73: 204 134.73 - 143.73: 6 Bond angle restraints: 21000 Sorted by residual: angle pdb=" CA LEU A 240 " pdb=" CB LEU A 240 " pdb=" CG LEU A 240 " ideal model delta sigma weight residual 116.30 102.04 14.26 3.50e+00 8.16e-02 1.66e+01 angle pdb=" CA LEU C 240 " pdb=" CB LEU C 240 " pdb=" CG LEU C 240 " ideal model delta sigma weight residual 116.30 102.06 14.24 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CA LEU F 240 " pdb=" CB LEU F 240 " pdb=" CG LEU F 240 " ideal model delta sigma weight residual 116.30 102.07 14.23 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CA LEU B 240 " pdb=" CB LEU B 240 " pdb=" CG LEU B 240 " ideal model delta sigma weight residual 116.30 102.12 14.18 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA LEU E 240 " pdb=" CB LEU E 240 " pdb=" CG LEU E 240 " ideal model delta sigma weight residual 116.30 102.12 14.18 3.50e+00 8.16e-02 1.64e+01 ... (remaining 20995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 8893 15.15 - 30.30: 387 30.30 - 45.46: 110 45.46 - 60.61: 12 60.61 - 75.76: 30 Dihedral angle restraints: 9432 sinusoidal: 3756 harmonic: 5676 Sorted by residual: dihedral pdb=" CA PRO C 317 " pdb=" C PRO C 317 " pdb=" N GLY C 318 " pdb=" CA GLY C 318 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO F 317 " pdb=" C PRO F 317 " pdb=" N GLY F 318 " pdb=" CA GLY F 318 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO E 317 " pdb=" C PRO E 317 " pdb=" N GLY E 318 " pdb=" CA GLY E 318 " ideal model delta harmonic sigma weight residual 180.00 -156.20 -23.80 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2086 0.091 - 0.183: 337 0.183 - 0.274: 19 0.274 - 0.365: 0 0.365 - 0.457: 6 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CG LEU E 240 " pdb=" CB LEU E 240 " pdb=" CD1 LEU E 240 " pdb=" CD2 LEU E 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.45 2.00e-01 2.50e+01 5.17e+00 ... (remaining 2445 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 105 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C GLU C 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU C 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR C 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 105 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLU F 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU F 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR F 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 105 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLU A 105 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 105 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 106 " 0.014 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3966 2.81 - 3.33: 12905 3.33 - 3.86: 24340 3.86 - 4.38: 27441 4.38 - 4.90: 48134 Nonbonded interactions: 116786 Sorted by model distance: nonbonded pdb=" O ARG B 103 " pdb=" OG1 THR B 106 " model vdw 2.289 2.440 nonbonded pdb=" O ARG E 103 " pdb=" OG1 THR E 106 " model vdw 2.289 2.440 nonbonded pdb=" O ARG D 103 " pdb=" OG1 THR D 106 " model vdw 2.289 2.440 nonbonded pdb=" O ARG F 103 " pdb=" OG1 THR F 106 " model vdw 2.289 2.440 nonbonded pdb=" O ARG C 103 " pdb=" OG1 THR C 106 " model vdw 2.290 2.440 ... (remaining 116781 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 5.320 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 40.190 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.008 0.072 15498 Z= 0.538 Angle : 1.162 23.020 21000 Z= 0.594 Chirality : 0.067 0.457 2448 Planarity : 0.008 0.058 2736 Dihedral : 11.009 75.760 5808 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -2.93 (0.15), residues: 1998 helix: -3.43 (0.21), residues: 192 sheet: -1.13 (0.20), residues: 570 loop : -2.18 (0.14), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 109 HIS 0.005 0.002 HIS A 164 PHE 0.042 0.005 PHE C 221 TYR 0.018 0.003 TYR D 68 ARG 0.005 0.001 ARG E 374 *********************** 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 403 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8013 (tt) cc_final: 0.7784 (tp) REVERT: A 190 TYR cc_start: 0.8795 (t80) cc_final: 0.8391 (t80) REVERT: A 314 ASP cc_start: 0.7563 (m-30) cc_final: 0.7362 (m-30) REVERT: B 134 MET cc_start: 0.7804 (ptm) cc_final: 0.7529 (ptp) REVERT: C 54 MET cc_start: 0.6363 (mtp) cc_final: 0.5778 (mmm) REVERT: C 87 LYS cc_start: 0.7115 (ttmp) cc_final: 0.6621 (tppt) REVERT: C 110 LEU cc_start: 0.9013 (tp) cc_final: 0.8777 (tp) REVERT: C 114 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8558 (mttm) REVERT: C 144 HIS cc_start: 0.7732 (t-90) cc_final: 0.7384 (t70) REVERT: C 190 TYR cc_start: 0.8867 (t80) cc_final: 0.8500 (t80) REVERT: D 107 GLN cc_start: 0.7595 (mt0) cc_final: 0.7304 (mm110) REVERT: D 117 LEU cc_start: 0.7908 (tt) cc_final: 0.7688 (tp) REVERT: D 190 TYR cc_start: 0.8796 (t80) cc_final: 0.8386 (t80) REVERT: E 134 MET cc_start: 0.7790 (ptm) cc_final: 0.7553 (ptp) REVERT: F 87 LYS cc_start: 0.7213 (ttmp) cc_final: 0.6761 (tppt) REVERT: F 110 LEU cc_start: 0.9011 (tp) cc_final: 0.8771 (tp) REVERT: F 114 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8582 (mttm) REVERT: F 144 HIS cc_start: 0.7680 (t-90) cc_final: 0.7395 (t70) REVERT: F 190 TYR cc_start: 0.8846 (t80) cc_final: 0.8481 (t80) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2849 time to fit residues: 164.9372 Evaluate side-chains 233 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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: 3.9990 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 164 HIS A 316 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 174 ASN B 316 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 166 GLN C 316 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 164 HIS D 316 ASN D 345 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN E 174 ASN E 316 ASN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 166 GLN F 316 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15498 Z= 0.232 Angle : 0.687 16.965 21000 Z= 0.332 Chirality : 0.047 0.197 2448 Planarity : 0.005 0.037 2736 Dihedral : 5.214 16.631 2136 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 3.56 % Allowed : 9.67 % Favored : 86.77 % 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: -2.28 (0.17), residues: 1998 helix: -2.47 (0.29), residues: 198 sheet: -0.97 (0.17), residues: 750 loop : -1.70 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 222 HIS 0.003 0.001 HIS B 164 PHE 0.016 0.002 PHE A 364 TYR 0.010 0.001 TYR F 154 ARG 0.005 0.000 ARG C 155 *********************** 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 306 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 246 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 107 GLN cc_start: 0.8189 (mm110) cc_final: 0.7863 (mt0) REVERT: A 135 MET cc_start: 0.6600 (mtt) cc_final: 0.6242 (ttm) REVERT: A 166 GLN cc_start: 0.7566 (mt0) cc_final: 0.7294 (mt0) REVERT: A 195 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7975 (p0) REVERT: A 314 ASP cc_start: 0.7447 (m-30) cc_final: 0.7148 (m-30) REVERT: B 69 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7563 (mt0) REVERT: B 98 MET cc_start: 0.7982 (tpp) cc_final: 0.7596 (tpp) REVERT: C 54 MET cc_start: 0.6171 (mtp) cc_final: 0.5669 (mmm) REVERT: C 87 LYS cc_start: 0.6836 (ttmp) cc_final: 0.6622 (tppt) REVERT: C 114 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8422 (mttm) REVERT: C 166 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7020 (mt0) REVERT: C 190 TYR cc_start: 0.8527 (t80) cc_final: 0.8138 (t80) REVERT: C 195 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7894 (p0) REVERT: D 105 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 190 TYR cc_start: 0.8495 (t80) cc_final: 0.8259 (t80) REVERT: D 195 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.8002 (p0) REVERT: F 114 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8428 (mttm) REVERT: F 166 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: F 190 TYR cc_start: 0.8506 (t80) cc_final: 0.8121 (t80) REVERT: F 195 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7897 (p0) outliers start: 60 outliers final: 28 residues processed: 291 average time/residue: 0.2632 time to fit residues: 112.7043 Evaluate side-chains 245 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 180 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN E 69 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15498 Z= 0.245 Angle : 0.640 13.247 21000 Z= 0.314 Chirality : 0.047 0.169 2448 Planarity : 0.004 0.035 2736 Dihedral : 4.933 18.791 2136 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.03 % Allowed : 11.09 % Favored : 84.88 % 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: -1.90 (0.17), residues: 1998 helix: -1.64 (0.34), residues: 198 sheet: -0.69 (0.18), residues: 738 loop : -1.58 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 222 HIS 0.006 0.001 HIS F 164 PHE 0.015 0.002 PHE D 253 TYR 0.016 0.001 TYR B 131 ARG 0.004 0.000 ARG F 155 *********************** 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 293 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 225 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 107 GLN cc_start: 0.8263 (mm110) cc_final: 0.7922 (mt0) REVERT: A 195 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7892 (p0) REVERT: A 314 ASP cc_start: 0.7461 (m-30) cc_final: 0.7185 (m-30) REVERT: B 69 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7653 (mt0) REVERT: C 87 LYS cc_start: 0.6988 (ttmp) cc_final: 0.6709 (tppt) REVERT: C 114 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8432 (mttm) REVERT: C 166 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: C 190 TYR cc_start: 0.8403 (t80) cc_final: 0.8010 (t80) REVERT: D 190 TYR cc_start: 0.8449 (t80) cc_final: 0.8248 (t80) REVERT: D 195 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7894 (p0) REVERT: F 114 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8392 (mttm) REVERT: F 166 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: F 190 TYR cc_start: 0.8372 (t80) cc_final: 0.7994 (t80) outliers start: 68 outliers final: 45 residues processed: 280 average time/residue: 0.2851 time to fit residues: 117.2655 Evaluate side-chains 256 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN B 338 ASN C 69 GLN C 107 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 166 GLN D 47 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 77 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15498 Z= 0.311 Angle : 0.660 12.316 21000 Z= 0.327 Chirality : 0.048 0.174 2448 Planarity : 0.004 0.030 2736 Dihedral : 4.963 19.013 2136 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.45 % Allowed : 11.27 % Favored : 84.28 % 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: -1.98 (0.17), residues: 1998 helix: -1.80 (0.33), residues: 234 sheet: -0.40 (0.19), residues: 666 loop : -1.81 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 222 HIS 0.006 0.001 HIS F 164 PHE 0.016 0.002 PHE A 253 TYR 0.016 0.002 TYR B 131 ARG 0.004 0.001 ARG F 155 *********************** 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 276 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 201 time to evaluate : 1.932 Fit side-chains REVERT: A 107 GLN cc_start: 0.8296 (mm110) cc_final: 0.7859 (mt0) REVERT: A 195 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 314 ASP cc_start: 0.7506 (m-30) cc_final: 0.7245 (m-30) REVERT: C 87 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6774 (tppt) REVERT: C 105 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 107 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: C 114 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8463 (mttm) REVERT: C 124 ASP cc_start: 0.7900 (t0) cc_final: 0.7594 (t0) REVERT: C 166 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: C 190 TYR cc_start: 0.8500 (t80) cc_final: 0.8095 (t80) REVERT: C 195 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8041 (p0) REVERT: D 195 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.7890 (p0) REVERT: F 114 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8483 (mttm) REVERT: F 166 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: F 190 TYR cc_start: 0.8471 (t80) cc_final: 0.8096 (t80) REVERT: F 195 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8065 (p0) outliers start: 75 outliers final: 60 residues processed: 261 average time/residue: 0.2723 time to fit residues: 105.1077 Evaluate side-chains 260 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 192 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0470 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15498 Z= 0.226 Angle : 0.604 12.025 21000 Z= 0.299 Chirality : 0.046 0.180 2448 Planarity : 0.004 0.030 2736 Dihedral : 4.744 18.409 2136 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.51 % Allowed : 12.22 % Favored : 83.27 % 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: -1.48 (0.18), residues: 1998 helix: -0.97 (0.38), residues: 198 sheet: -0.04 (0.20), residues: 630 loop : -1.57 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 222 HIS 0.006 0.001 HIS B 144 PHE 0.014 0.002 PHE D 253 TYR 0.018 0.001 TYR D 154 ARG 0.005 0.000 ARG C 155 *********************** 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 283 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 207 time to evaluate : 1.859 Fit side-chains REVERT: A 107 GLN cc_start: 0.8295 (mm110) cc_final: 0.7814 (mt0) REVERT: A 195 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8308 (p0) REVERT: A 314 ASP cc_start: 0.7496 (m-30) cc_final: 0.7258 (m-30) REVERT: B 204 ASP cc_start: 0.7366 (p0) cc_final: 0.7072 (p0) REVERT: C 87 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6733 (tppt) REVERT: C 105 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7182 (tm-30) REVERT: C 114 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8440 (mttm) REVERT: C 166 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: C 190 TYR cc_start: 0.8436 (t80) cc_final: 0.8040 (t80) REVERT: C 195 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8010 (p0) REVERT: D 195 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8252 (p0) REVERT: E 69 GLN cc_start: 0.8050 (mp10) cc_final: 0.7826 (mt0) REVERT: E 204 ASP cc_start: 0.7343 (p0) cc_final: 0.7067 (p0) REVERT: F 114 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8465 (mttm) REVERT: F 166 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: F 190 TYR cc_start: 0.8371 (t80) cc_final: 0.7981 (t80) REVERT: F 195 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.7991 (p0) outliers start: 76 outliers final: 57 residues processed: 269 average time/residue: 0.2655 time to fit residues: 105.6396 Evaluate side-chains 263 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15498 Z= 0.244 Angle : 0.610 11.963 21000 Z= 0.303 Chirality : 0.046 0.199 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.706 17.838 2136 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.39 % Allowed : 13.64 % Favored : 81.97 % 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: -1.40 (0.18), residues: 1998 helix: -0.86 (0.39), residues: 198 sheet: -0.31 (0.19), residues: 702 loop : -1.35 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 109 HIS 0.005 0.001 HIS F 164 PHE 0.014 0.001 PHE D 253 TYR 0.019 0.002 TYR D 154 ARG 0.005 0.000 ARG C 155 *********************** 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 280 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 206 time to evaluate : 1.788 Fit side-chains REVERT: A 107 GLN cc_start: 0.8313 (mm110) cc_final: 0.7805 (mt0) REVERT: A 314 ASP cc_start: 0.7442 (m-30) cc_final: 0.7204 (m-30) REVERT: B 104 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 204 ASP cc_start: 0.7377 (p0) cc_final: 0.7056 (p0) REVERT: C 87 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6745 (tppt) REVERT: C 105 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7157 (tm-30) REVERT: C 114 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8426 (mttm) REVERT: C 124 ASP cc_start: 0.7898 (t0) cc_final: 0.7582 (t0) REVERT: C 166 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: C 190 TYR cc_start: 0.8439 (t80) cc_final: 0.8059 (t80) REVERT: C 195 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7974 (p0) REVERT: D 195 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8266 (p0) REVERT: E 68 TYR cc_start: 0.8038 (t80) cc_final: 0.7637 (t80) REVERT: E 69 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: E 204 ASP cc_start: 0.7358 (p0) cc_final: 0.7047 (p0) REVERT: F 98 MET cc_start: 0.8107 (tpp) cc_final: 0.7874 (tpp) REVERT: F 105 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7177 (tm-30) REVERT: F 114 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8445 (mttm) REVERT: F 166 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: F 190 TYR cc_start: 0.8376 (t80) cc_final: 0.7997 (t80) REVERT: F 195 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8089 (p0) outliers start: 74 outliers final: 63 residues processed: 265 average time/residue: 0.2688 time to fit residues: 105.1959 Evaluate side-chains 267 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 197 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 370 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN D 130 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15498 Z= 0.330 Angle : 0.659 11.606 21000 Z= 0.327 Chirality : 0.047 0.184 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.921 19.352 2136 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.33 % Allowed : 14.41 % Favored : 81.26 % 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: -1.73 (0.18), residues: 1998 helix: -1.51 (0.34), residues: 234 sheet: -0.28 (0.19), residues: 666 loop : -1.64 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 109 HIS 0.002 0.001 HIS E 164 PHE 0.016 0.002 PHE D 253 TYR 0.020 0.002 TYR F 131 ARG 0.005 0.001 ARG C 155 *********************** 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 274 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 201 time to evaluate : 1.692 Fit side-chains REVERT: A 107 GLN cc_start: 0.8341 (mm110) cc_final: 0.7811 (mt0) REVERT: A 314 ASP cc_start: 0.7543 (m-30) cc_final: 0.7292 (m-30) REVERT: B 68 TYR cc_start: 0.7938 (t80) cc_final: 0.7360 (t80) REVERT: B 104 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 204 ASP cc_start: 0.7409 (p0) cc_final: 0.7098 (p0) REVERT: C 87 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6729 (tppt) REVERT: C 105 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7178 (tm-30) REVERT: C 114 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8426 (mttm) REVERT: C 124 ASP cc_start: 0.7865 (t0) cc_final: 0.7523 (t0) REVERT: C 190 TYR cc_start: 0.8502 (t80) cc_final: 0.8134 (t80) REVERT: C 195 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8023 (p0) REVERT: D 135 MET cc_start: 0.7167 (ttm) cc_final: 0.6903 (ttm) REVERT: D 195 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8257 (p0) REVERT: E 68 TYR cc_start: 0.8206 (t80) cc_final: 0.7961 (t80) REVERT: E 69 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: E 204 ASP cc_start: 0.7393 (p0) cc_final: 0.7085 (p0) REVERT: F 105 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7183 (tm-30) REVERT: F 114 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8455 (mttm) REVERT: F 190 TYR cc_start: 0.8484 (t80) cc_final: 0.8118 (t80) REVERT: F 195 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8093 (p0) outliers start: 73 outliers final: 61 residues processed: 261 average time/residue: 0.2700 time to fit residues: 103.5642 Evaluate side-chains 260 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 370 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15498 Z= 0.187 Angle : 0.584 11.863 21000 Z= 0.290 Chirality : 0.045 0.171 2448 Planarity : 0.004 0.031 2736 Dihedral : 4.490 16.889 2136 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 3.97 % Allowed : 14.95 % Favored : 81.08 % 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: -1.39 (0.18), residues: 1998 helix: -0.85 (0.39), residues: 204 sheet: -0.13 (0.20), residues: 642 loop : -1.43 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 109 HIS 0.002 0.001 HIS E 164 PHE 0.012 0.001 PHE A 253 TYR 0.029 0.002 TYR F 68 ARG 0.005 0.000 ARG C 155 *********************** 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 271 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 204 time to evaluate : 1.689 Fit side-chains REVERT: A 107 GLN cc_start: 0.8263 (mm110) cc_final: 0.7776 (mt0) REVERT: A 144 HIS cc_start: 0.7290 (t-170) cc_final: 0.6097 (m-70) REVERT: A 191 ASP cc_start: 0.7424 (t70) cc_final: 0.7123 (t0) REVERT: A 314 ASP cc_start: 0.7444 (m-30) cc_final: 0.7214 (m-30) REVERT: B 68 TYR cc_start: 0.7728 (t80) cc_final: 0.7090 (t80) REVERT: B 104 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 204 ASP cc_start: 0.7245 (p0) cc_final: 0.6955 (p0) REVERT: C 114 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8390 (mttm) REVERT: C 190 TYR cc_start: 0.8346 (t80) cc_final: 0.7947 (t80) REVERT: C 195 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7931 (p0) REVERT: E 204 ASP cc_start: 0.7234 (p0) cc_final: 0.6927 (p0) REVERT: F 114 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8336 (mttm) REVERT: F 190 TYR cc_start: 0.8353 (t80) cc_final: 0.7981 (t80) REVERT: F 195 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8021 (p0) outliers start: 67 outliers final: 59 residues processed: 257 average time/residue: 0.2669 time to fit residues: 101.3328 Evaluate side-chains 252 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 191 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 370 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 166 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 168 optimal weight: 0.0040 chunk 116 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15498 Z= 0.172 Angle : 0.597 11.922 21000 Z= 0.299 Chirality : 0.045 0.188 2448 Planarity : 0.004 0.030 2736 Dihedral : 4.305 16.541 2136 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.74 % Allowed : 15.42 % Favored : 80.84 % 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: -1.33 (0.18), residues: 1998 helix: -0.72 (0.39), residues: 204 sheet: -0.06 (0.20), residues: 672 loop : -1.45 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 109 HIS 0.001 0.000 HIS C 144 PHE 0.013 0.001 PHE C 253 TYR 0.025 0.002 TYR F 68 ARG 0.006 0.000 ARG F 155 *********************** 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 263 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 200 time to evaluate : 1.928 Fit side-chains REVERT: A 54 MET cc_start: 0.6157 (mtt) cc_final: 0.5515 (tpp) REVERT: A 107 GLN cc_start: 0.8272 (mm110) cc_final: 0.7879 (mt0) REVERT: A 144 HIS cc_start: 0.7364 (t-170) cc_final: 0.6186 (m-70) REVERT: A 191 ASP cc_start: 0.7373 (t70) cc_final: 0.7117 (t0) REVERT: A 314 ASP cc_start: 0.7413 (m-30) cc_final: 0.7200 (m-30) REVERT: B 68 TYR cc_start: 0.7675 (t80) cc_final: 0.6999 (t80) REVERT: B 104 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 114 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8209 (mttm) REVERT: C 190 TYR cc_start: 0.8375 (t80) cc_final: 0.7986 (t80) REVERT: C 195 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7872 (p0) REVERT: D 144 HIS cc_start: 0.7371 (t-170) cc_final: 0.6283 (m90) REVERT: F 114 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8233 (mttm) REVERT: F 190 TYR cc_start: 0.8326 (t80) cc_final: 0.7957 (t80) REVERT: F 195 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7918 (p0) outliers start: 63 outliers final: 56 residues processed: 249 average time/residue: 0.2609 time to fit residues: 96.3862 Evaluate side-chains 249 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 191 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 370 ASP 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: 0.3980 chunk 89 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15498 Z= 0.155 Angle : 0.589 11.921 21000 Z= 0.293 Chirality : 0.044 0.176 2448 Planarity : 0.004 0.031 2736 Dihedral : 4.101 16.250 2136 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.85 % Allowed : 16.79 % Favored : 80.37 % 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: -1.25 (0.18), residues: 1998 helix: -0.61 (0.39), residues: 204 sheet: -0.00 (0.20), residues: 672 loop : -1.41 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 109 HIS 0.001 0.000 HIS B 164 PHE 0.012 0.001 PHE C 253 TYR 0.031 0.002 TYR D 68 ARG 0.006 0.000 ARG F 155 ********************** 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 248 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.612 Fit side-chains REVERT: A 107 GLN cc_start: 0.8223 (mm110) cc_final: 0.7909 (mt0) REVERT: A 144 HIS cc_start: 0.7359 (t-170) cc_final: 0.6235 (m-70) REVERT: A 191 ASP cc_start: 0.7285 (t70) cc_final: 0.7058 (t0) REVERT: B 104 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 107 GLN cc_start: 0.8038 (mt0) cc_final: 0.7709 (mt0) REVERT: B 144 HIS cc_start: 0.7695 (t-170) cc_final: 0.6216 (m-70) REVERT: C 114 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8206 (mttm) REVERT: C 131 TYR cc_start: 0.9070 (p90) cc_final: 0.8824 (p90) REVERT: C 190 TYR cc_start: 0.8310 (t80) cc_final: 0.7927 (t80) REVERT: C 195 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7792 (p0) REVERT: D 144 HIS cc_start: 0.7488 (t-170) cc_final: 0.6321 (m90) REVERT: D 195 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8196 (p0) REVERT: F 114 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8240 (mttm) REVERT: F 190 TYR cc_start: 0.8278 (t80) cc_final: 0.7917 (t80) REVERT: F 195 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7822 (p0) outliers start: 48 outliers final: 43 residues processed: 238 average time/residue: 0.2597 time to fit residues: 91.6797 Evaluate side-chains 227 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN A 174 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112752 restraints weight = 22866.448| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.83 r_work: 0.3177 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15498 Z= 0.197 Angle : 0.612 11.855 21000 Z= 0.305 Chirality : 0.045 0.179 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.229 15.478 2136 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.97 % Allowed : 17.02 % Favored : 80.01 % 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: -1.27 (0.18), residues: 1998 helix: -0.82 (0.38), residues: 210 sheet: 0.00 (0.20), residues: 642 loop : -1.36 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 109 HIS 0.002 0.000 HIS B 164 PHE 0.013 0.001 PHE D 253 TYR 0.030 0.002 TYR A 68 ARG 0.006 0.000 ARG C 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3280.80 seconds wall clock time: 60 minutes 11.40 seconds (3611.40 seconds total)