Starting phenix.real_space_refine on Thu Nov 16 12:07:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/11_2023/6v0g_20997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/11_2023/6v0g_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_20997/11_2023/6v0g_20997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/11_2023/6v0g_20997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/11_2023/6v0g_20997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0g_20997/11_2023/6v0g_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-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "D" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "E" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain: "F" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2542 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Time building chain proxies: 8.12, per 1000 atoms: 0.53 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: 5.54 Conformation dependent library (CDL) restraints added in 3.3 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: 2.17 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: 5.46 Time building geometry restraints manager: 6.01 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: 1.800 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: 5.370 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 42.890 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2861 time to fit residues: 165.8848 Evaluate side-chains 228 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8930 ------------------------------------------------------------------------------- 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: 0.9980 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15498 Z= 0.222 Angle : 0.681 16.895 21000 Z= 0.329 Chirality : 0.047 0.195 2448 Planarity : 0.005 0.037 2736 Dihedral : 5.183 16.693 2136 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 3.50 % Allowed : 9.91 % Favored : 86.60 % 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: -2.51 (0.28), residues: 198 sheet: -0.96 (0.17), residues: 750 loop : -1.69 (0.17), residues: 1050 *********************** 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 303 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 244 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 289 average time/residue: 0.2670 time to fit residues: 113.0660 Evaluate side-chains 237 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1292 time to fit residues: 9.1369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 180 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 107 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 166 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15498 Z= 0.174 Angle : 0.600 13.573 21000 Z= 0.294 Chirality : 0.045 0.156 2448 Planarity : 0.004 0.036 2736 Dihedral : 4.675 17.125 2136 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.19 % Allowed : 11.98 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 1998 helix: -1.58 (0.34), residues: 198 sheet: -0.42 (0.18), residues: 702 loop : -1.66 (0.17), residues: 1098 *********************** 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 263 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 1.882 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 255 average time/residue: 0.2999 time to fit residues: 109.4439 Evaluate side-chains 218 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1298 time to fit residues: 7.6123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0870 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN D 47 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** 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: 0.8002 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15498 Z= 0.180 Angle : 0.589 12.685 21000 Z= 0.291 Chirality : 0.045 0.148 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.452 15.877 2136 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 12.46 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.18), residues: 1998 helix: -1.11 (0.37), residues: 198 sheet: -0.38 (0.19), residues: 702 loop : -1.50 (0.18), residues: 1098 *********************** 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 250 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 1.672 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 239 average time/residue: 0.2948 time to fit residues: 100.9069 Evaluate side-chains 212 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1392 time to fit residues: 7.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0010 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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** A 144 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15498 Z= 0.473 Angle : 0.763 14.188 21000 Z= 0.378 Chirality : 0.050 0.176 2448 Planarity : 0.005 0.043 2736 Dihedral : 5.401 22.187 2136 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.78 % Allowed : 14.89 % Favored : 83.33 % 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: -2.01 (0.18), residues: 1998 helix: -1.93 (0.32), residues: 246 sheet: -0.47 (0.19), residues: 696 loop : -1.79 (0.18), residues: 1056 *********************** 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 235 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.606 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 231 average time/residue: 0.2976 time to fit residues: 98.4190 Evaluate side-chains 201 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1334 time to fit residues: 6.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 144 HIS B 47 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN C 47 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 164 HIS F 309 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15498 Z= 0.187 Angle : 0.604 11.902 21000 Z= 0.300 Chirality : 0.045 0.155 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.621 18.639 2136 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.01 % Allowed : 16.31 % Favored : 82.68 % 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: -1.49 (0.18), residues: 1998 helix: -1.23 (0.37), residues: 210 sheet: -0.33 (0.19), residues: 702 loop : -1.38 (0.19), residues: 1086 *********************** 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 218 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.793 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 213 average time/residue: 0.2892 time to fit residues: 89.4611 Evaluate side-chains 203 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1399 time to fit residues: 5.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15498 Z= 0.301 Angle : 0.647 11.753 21000 Z= 0.320 Chirality : 0.047 0.163 2448 Planarity : 0.004 0.029 2736 Dihedral : 4.825 18.793 2136 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.95 % Allowed : 17.67 % Favored : 81.38 % 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: -1.77 (0.18), residues: 1998 helix: -1.72 (0.33), residues: 246 sheet: -0.11 (0.20), residues: 630 loop : -1.72 (0.17), residues: 1122 *********************** 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 212 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 196 time to evaluate : 1.823 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 207 average time/residue: 0.3005 time to fit residues: 89.3465 Evaluate side-chains 195 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1309 time to fit residues: 4.7422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15498 Z= 0.240 Angle : 0.617 11.791 21000 Z= 0.307 Chirality : 0.046 0.175 2448 Planarity : 0.004 0.030 2736 Dihedral : 4.661 18.244 2136 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.07 % Allowed : 17.62 % Favored : 81.32 % 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: -0.78 (0.39), residues: 198 sheet: -0.21 (0.20), residues: 642 loop : -1.39 (0.18), residues: 1158 *********************** 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 213 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.900 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 208 average time/residue: 0.3057 time to fit residues: 91.7901 Evaluate side-chains 199 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1444 time to fit residues: 6.1623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 160 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 338 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15498 Z= 0.325 Angle : 0.666 11.882 21000 Z= 0.331 Chirality : 0.047 0.184 2448 Planarity : 0.004 0.031 2736 Dihedral : 4.887 19.156 2136 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.53 % Allowed : 17.85 % Favored : 81.61 % 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: -1.61 (0.18), residues: 1998 helix: -1.46 (0.34), residues: 234 sheet: -0.12 (0.20), residues: 600 loop : -1.53 (0.17), residues: 1164 *********************** 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 202 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.839 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 199 average time/residue: 0.3053 time to fit residues: 87.7491 Evaluate side-chains 193 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1398 time to fit residues: 4.4706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN ** F 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15498 Z= 0.175 Angle : 0.585 11.789 21000 Z= 0.291 Chirality : 0.045 0.162 2448 Planarity : 0.004 0.032 2736 Dihedral : 4.403 16.745 2136 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 18.27 % Favored : 81.73 % 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: -1.18 (0.18), residues: 1998 helix: -0.63 (0.39), residues: 198 sheet: -0.02 (0.21), residues: 600 loop : -1.24 (0.17), residues: 1200 ********************** 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 197 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.786 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3039 time to fit residues: 86.1961 Evaluate side-chains 185 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.7980 chunk 48 optimal weight: 0.0470 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 161 optimal weight: 0.2980 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 151 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 = 0.3825 r_free = 0.3825 target = 0.144197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112428 restraints weight = 22376.003| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.68 r_work: 0.3191 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15498 Z= 0.192 Angle : 0.601 11.948 21000 Z= 0.299 Chirality : 0.045 0.166 2448 Planarity : 0.004 0.032 2736 Dihedral : 4.393 15.936 2136 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.06 % Allowed : 19.69 % Favored : 80.25 % 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: -1.13 (0.18), residues: 1998 helix: -0.62 (0.39), residues: 198 sheet: 0.03 (0.21), residues: 600 loop : -1.21 (0.17), residues: 1200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.74 seconds wall clock time: 60 minutes 17.54 seconds (3617.54 seconds total)